A Bay Area pediatrician and former foster parent who has been accused of sexual molestation by more than a dozen children and teens since 2001 is under investigation for a third time, after a new allegation of abuse in Santa Cruz County.

The investigation of Dr. Patrick Clyne, 57, who practices in the small community of Freedom, is a joint effort by the Medical Board of California and the Watsonville Police Department, police officials said. It involves a complaint from a child patient that was first reported to the Santa Cruz County Sheriff’s Office in May.

The new investigation comes eight years after a succession of complaints of sexual abuse made against Clyne, the former chief pediatrician for children in Santa Clara County’s foster care system. Hundreds of pages of filings in a U.S. District Court case show that between 2009 and 2011, 10 of Clyne’s former patients — foster children he treated at a county shelter — reported examinations so invasive other physicians described them as “extraordinarily uncommon,” “bizarre” and “suspicious.”

Years earlier, three boys placed in Clyne’s South Bay homes as foster children also reported being repeatedly molested by him, with one boy describing as many as 11 incidents of sexual abuse. Those allegations were presented to a criminal grand jury but did not lead to an indictment.

Watsonville police officials said they could not release additional information about the latest complaint “because of the sensitive nature of the case” and because it involves a juvenile. The Medical Board, which licenses and can suspend doctors, said its investigations are kept confidential by law and would not confirm anything related to the case.

The new case raises questions about how Clyne, who after the earlier allegations was suspended twice and ultimately fired from Santa Clara County’s public hospital and barred from parenting foster youth, has been allowed to continue to practice.

In an interview, Clyne said he did not know about the latest allegation so could not respond to it. He said the allegations made in 2001 by the foster boys who had lived with him were lies, and that the child patients who reported him must have misinterpreted his examinations because of their mistrust of adults or histories of abuse.

“My past has been investigated a lot, and there hasn’t been a time that a D.A. felt there was enough evidence to sustain a charge. Because of that, I’ve never been arrested for these allegations,” Clyne said. “It’s hard for me to know why people would say these things occurred.”

Yet previously confidential court documents show that police detectives repeatedly recommended that prosecutors file criminal charges against Clyne. The documents also show that Child Protective Services in Santa Clara County received numerous calls reporting allegations of sexual abuse. A wide range of professionals made the reports after hearing from children in their care, including social workers, parents and guardians, therapists, a juvenile probation officer and staff at two residential group homes in the South Bay.

The Medical Board of California has never placed restrictions on Clyne’s ability to practice medicine. But Clyne could not obtain a medical license in New Mexico in 2012 when that state’s medical board discovered he had not informed it about the numerous allegations of sexual abuse against him and the disciplinary actions that followed.

In an unrelated action two years later, the California Department of Social Services banned Clyne from ever parenting foster youth and from working with any children or adults in state-licensed care facilities.

Tonya Batorski, who said her son testified in 2002 before a Santa Clara County criminal grand jury that he was abused by Clyne, was angered when she learned that a new allegation has been made against the pediatrician.

“It’s hard to wrap my mind around somebody getting away with this for so long, and to continue to work with the most vulnerable of our society when they know he has had multiple allegations,” said Batorski. “Everybody’s involved for giving him his license knowing about his past — they’re at fault as well.”

Clyne’s connection to the foster care system dates to 1994, public records show, when he became a foster parent to the first of four young boys who would live with him over the next several years. In 1996, he became the chief pediatrician for children in foster care in Santa Clara County, seeing patients at the Santa Clara Valley Medical Center in San Jose and at the county children’s shelter.

In his capacity examining and treating abused and neglected children, Clyne also served as an expert witness for the Santa Clara County district attorney’s office for several years during his time at the public hospital.

Throughout his career, Clyne has earned professional respect. During a rock-climbing trip on the Appalachian Trail in his second year of medical residency, he fell 20 feet off a cliff and severed his spinal cord. After eight months in rehabilitation, Clyne nonetheless managed to complete his residency and a Stanford University fellowship, and now treats patients from a wheelchair.

Clyne has been praised in the past by colleagues and foster parents for his commitment to vulnerable children and round-the-clock availability, including two adoptive parents who Clyne said have continued to bring their children to see him since he moved his practice from Santa Clara to Santa Cruz County. Before the allegations against him became public, he was honored at a 2007 luncheon of the Legal Advocates for Children and Youth, the law firm representing children in the Santa Clara County foster care system.

But twice during his 16-year Santa Clara County tenure, Clyne was placed on administrative leave while under investigation by the police and sheriff’s departments.

The first investigation occurred in 2001, court records show, and involved three of the boys in foster care who were placed in Clyne’s home and reported to local law enforcement that he repeatedly molested them. In agonized disclosures, two of the boys said they were in third, fourth and fifth grades when they were awakened by Clyne’s groping, and described the confusion and torment that resulted. The third youth, who spent a shorter period of time with Clyne as an older foster teen, told police he was groped in a manner that Clyne would then pretend was a slip of his hand, and he was willing to testify in court about it.

The Chronicle is not identifying the former foster youth because it does not identify alleged victims of sexual assault.

One boy’s account describes his waking up to Clyne reaching inside his boxer shorts. After he knocked Clyne’s hand away, he said: “He’s like, it fell out of your boxers, I’m just putting it away,” the boy recalled.

One of the boys “couldn’t stop crying or throwing up” as he recounted the abuse to his mother, and “just kept saying, I’m sorry Mommy for letting him touch me,” the records show. Another boy said he’d felt so uncomfortable since his experiences with Clyne, “I can’t even hug my mom really long. It makes me sick just when people touch me.”

Clyne said in an interview that two of his foster boys would sleep in his bed at night, “but there would be no sexual contact.” In response to the third boy, Clyne said: “I can’t think of any interaction with him that would have been misinterpreted.”

After the 2001 police investigation, the Santa Clara County district attorney’s office brought a case before a grand jury. But in a development that continues to astound those familiar with the allegations against Clyne, no indictment was returned. Clyne returned to work at Valley Medical Center and continued treating children in the foster care system.

Eight years later, in November 2009, new allegations of abuse arose. Others followed in 2010 and 2011. San Jose police and the sheriff investigated again, and Clyne was again placed on administrative leave from his post at the public hospital.

The new allegations involved 10 boys and girls, some as young as age 8, whom Clyne had treated at the county children’s shelter. The children reported being molested by Clyne during routine wellness exams, according to police reports and Department of Family and Children’s Services internal documents.

The youngsters described being alone with the doctor when he touched their “private parts” and inserted his fingers inside the girls. One girl said “the doctor makes her ‘squat’ on the table like a ‘frog’ and touches her privates.” A boy demonstrated how “Dr. Clyne had rubbed him up and down,” a Child Protective Services report states.

In a recent interview, Clyne said he believes the children who accused him misinterpreted their exams, which he said were perfectly appropriate.

“I certainly didn’t sexually stimulate anybody” or “do anything where something is put inside the child,” he said. “I wish I had a chance to explain it to them, but I’ve never done anything in a medical examination that brought me sexual gratification or should be interpreted as a sexual assault.”

Clyne said that in his current practice, he sees children with another adult in the room, unless they are 14 or older and insist on being seen alone. Earlier in his career, he conceded, “I was making decisions that weren’t the best; I should have had adults in the room.” He also said that, in some instances, he may have had third parties present, but neglected to document that in the children’s files.

During the police investigation into the children’s allegations, six pediatric specialists who were consulted concerning proper medical procedure criticized the conduct the children described.

Pediatrician Martha Snider told police genital exams of young children involve a “quick visual inspection” and should take about “three seconds.” She called exams of young children naked and alone with a doctor “bizarre,” “suspicious” and “peculiar.”

Dr. James Crawford-Jakubiak, medical director of the Center for Child Protection at UCSF Benioff Children’s Hospital Oakland, told investigators it would be “extraordinarily uncommon” for parents or caregivers not to be present during exams of children in third grade and younger, and that anything physically invasive would be rare.

Records note that in at least three incidents, the children’s allegations were “sent to the district attorney’s office for review” and “forwarded to the District Attorney for charging.” But the second investigation of Clyne also concluded without charges.

Asked recently why no charges were brought, Assistant District Attorney Terry Harman noted in an email reply that the grand jury did not indict Clyne in 2002 and said that his office’s follow-up review “led to a determination that we could not prove the case beyond a reasonable doubt.”

Clyne again returned to work, but weeks later, in February 2011, Santa Clara County prosecutors placed Clyne on a list of expert witnesses who could have their credibility challenged in court because of misconduct. In a letter to defense attorneys, the district attorney’s office wrote: “There is substantial evidence that Dr. Clyne committed multiple crimes involving moral turpitude, specifically sexual assault.”

The next month, Santa Clara County fired Clyne from his hospital job.

By June, Clyne had applied for a medical license to practice in New Mexico, but did not include information about having been suspended and fired from work after the sexual abuse allegations. After the board informed him that it had learned those facts, Clyne ended up withdrawing his application.

Clyne said the questions posed on the application for the New Mexico license were “a little vague” and he may have misinterpreted some of the language used to refer to his professional history.

Until 2014, Clyne was still able to be a licensed foster parent in California. But that year, the California Department of Social Services took action that led to his being barred from ever applying for a foster care license again. The 2014 action prohibited Clyne from serving on a board of directors, as an officer or executive director of any state-licensed facility. He was also prohibited from applying to register with “TrustLine,” a database of in-home caregivers, nannies and babysitters who have cleared criminal background checks in California.

The Medical Board of California has been formally notified of concerns about Clyne since at least 2011, when Santa Clara County officials sent the board a letter informing officials he had been dismissed. The board, which has the authority to suspend a doctor’s license after an arrest or if it determines there is an immediate threat to a patient’s safety, has taken no disciplinary action against Clyne.

In recent years, Clyne has quietly taken up a private practice in the tiny community of Freedom. Located in a humble strip-mall-style medical plaza on Green Valley Road, his Pediatric Medical Group of Watsonville serves mostly Spanish-speaking families who receive public health benefits. The complaint made against Clyne in May involved a patient of that clinic, police said.

“At this point I can tell you that there is an active investigation involving us and the state Medical Board, but I can’t tell you much further because it’s an ongoing investigation,” said Watsonville police Sgt. Radovan Radich.

Santa Clara County Executive Jeff Smith, who terminated Clyne’s contract with the county in 2011 and whose office contacted the state medical board, said he was disturbed to learn that there is a new allegation against him.

“All along I was expecting a vigorous discipline from the medical board,” Smith said. “Obviously, they do their own investigation, and it’s confidential. But it surprised me nothing more was done and that he was still practicing in the region.”

Clyne said he was not aware of the most recent complaint against him until contacted by The Chronicle, and could not respond to information he does not have.

“I believe you when you say this is going on, it just surprises me that no one has come to me or paid me a visit,” Clyne said. With regard to the medical board, he added: “My license is fine because I’m not guilty of anything, and if the medical board is investigating me, I expect I will hear from them.”

Learning of the new allegation against Clyne brings up bitter memories for those who accused him in the past but were left frustrated by the outcome.

Two of Clyne’s former foster children who testified before the criminal grand jury left his home angry and deeply wounded.

Clyne took Max in as a foster child in 1995 just before his 10th birthday. The boy lived with him at his San Jose home until he ran away at age 13. When he was 16, Max told investigators about five to 10 times that he could recall Clyne touching his penis during his elementary school years. According to police, Max said Clyne sometimes gave him sleeping pills, though he wasn’t sure whether he did so to take advantage of him. He also said the two played a game when he was 12 years old to see who could drink the most gin and tonic.

Max struggled through repeated interviews with police. “He couldn’t understand why Pat would do this,” one report states, and asked an officer if he thought “Pat needed help.”

Clyne denied all Max’s allegations in a recent interview. “Of course I would never use a medication to knock a kid out, and of course I’d never give a kid alcohol,” he said. “I didn’t touch his penis. I don’t know what he’s talking about.”

Records show that Clyne denied in interviews with police that he spoke with Max during their 2001-02 investigation. But phone logs and reports of recorded calls show him speaking with Max repeatedly during the investigation. In one conversation he warned Max “this whole thing could be devastating to his career,” police records show.

“They can’t make you say something that didn’t happen,” he told Max.

“I know, but it did, yeah, it did happen though, but I don’t know what for,” Max responded.

In his recent interview, Clyne also insisted that he never spoke to police at length about the 2001 or the 2011 allegations, despite a San Jose Police Department report and a 66-page transcript of an interview he did with a detective, dated Jan. 2, 2002. He suggested the reports could have been fabricated.

“This is really scaring me,” Clyne said. “If all this is going on with fake documents, then I’m being set up. My memory is not that bad.”

San Jose Police Department spokeswoman Gina Tepoorten confirmed the documents were authentic.

After he left Clyne’s house, Max eventually returned to the care of his mother. Batorski had recovered from a mental health crisis that earlier had separated the two and had regained custody of the boy.

She said she had appreciated Clyne’s generosity at first; he allowed her frequent visits with Max and she felt welcome in his home. “Pat befriended me, I trusted him, so I can see how he’s still using that,” she said. “When a doctor in a wheelchair approaches you, you don’t think those kinds of things. You think, what a heroic person, giving back and helping children.”

But when Max returned to her home as a young teen, Batorski said, she saw the impact of his time in Clyne’s home. He had struggled in school and had been arrested. By age 17, Batorski said, it seemed her son was starting to get his life together — he had a car, a job and an amateur boxing license he kept tucked into a Bible highlighted with favorite passages. But he had also gotten involved in crime, and was shot and killed at age 17.

Kyle was another foster child of Clyne’s and became his adoptive son. He lived with the physician during the same period as Max, from 1995 through 1998, beginning when he was in fourth-grade. Kyle was 15 and had moved across the country when he reported to his mother and a juvenile probation officer that Clyne had molested him.

According to a report by a San Jose police investigator who flew to Pennsylvania to interview Kyle in 2001, he described 11 incidents beginning at age 9 in which Clyne would wake him and up and grope him. One molestation occurred on a trip to Disneyland, said Kyle, who describes the incidents as “nightmares.”

In his interviews at the time, Clyne denied the incidents and anything that “could have been misconstrued.” He repeated those assertions recently, and said both Max and Kyle had made up stories about him.

Kyle, now 33, is a foreman at a Northern California construction company. He said his life is on a better track than it once was, but that he remains agonized over his repeated attempts at obtaining some form of justice. As a young teen, he flew across the country to testify before a grand jury. Six years ago, he spoke up again when the second set of allegations against Clyne were made public.

Even after years in therapy for depression and post-traumatic stress, each time he’s asked to relive the experiences, he said, there has been a lengthy recovery time. He said it feels inconceivable that children are still being ushered into Clyne’s office.

“I just want him to stop hurting children — that’s it,” Kyle said. “I just don’t want him to have the chance to do that again. It just blows my mind how anybody can let this happen, and continue to let this happen.”

Karen de Sá is a San Francisco Chronicle staff writer. Email: kdesa@sfchronicle.com