The Indiana State Department of Health has been collecting babies’ blood and DNA without their parents’ permission since 1991, according to an investigation by a local news station. Now the state wants to know what to do with the blood samples.

When a baby is born in Indiana, as with other states, the state conducts a newborn screening test. A nurse or midwife takes a few drops of blood from the heel of each infant. The blood is collected on a specialized filter paper, which is then sent to the state's Newborn Screening Lab in downtown Indianapolis.

At the lab, researchers conduct tests on the blood for more than 50 medical disorders, including hypothyroidism, sickle cell disease and conditions where a child is unable to process certain nutrients. Parents and doctors are then notified of the results.

“All babies are screened, even if they look healthy, because some medical conditions cannot be seen by just looking at the baby,” the Centers for Disease Control and Prevention says. “Finding these conditions soon after birth can help prevent some serious problems, such as brain damage, organ damage, and even death.”

Indiana's Newborn Screening Program annually identifies about 200 children who have serious metabolic, genetic or endocrine conditions; detects genetic heart defects in another 45 babies; and identifies hearing loss in about 200 babies.

But along with the newborn screening, the ISDH has kept the leftover blood samples for possible use in medical research, according to an investigation by WTHR. And the state admits it never received parental permission to do so, making the samples unusable for research.

"No, we did nothing to notify parents," Bob Bowman, director of ISDH's Genomics & Newborn Screening Program, said to the Indiana NBC affiliate. "That's why we are struggling right now to try to figure out what is the best and most appropriate thing to do."

"I'm curious why they didn't share that," Mallory Ervin, the mother of a 4-year-old named Theo, said. "It now makes me think ‘what are they hiding?' As a parent, I'd absolutely like to know."

The samples are stored in 666 bankers boxes in a warehouse without temperature or humidity controls in Indianapolis.

"Right now we have samples dating back to 1991, so there are approximately 2.25 to 2.5 million samples currently being held," said Bowman. "We do have a lot."

Bowman says that the samples of dried blood have been detached from any identifying personal information, which are maintained in a separate computer database.

Since the samples cannot be used for research without parental consent, the state is trying to figure out what to do next.

"In medical research, you do need to get formal permission. You need to tell someone what you are planning to do. That was not happening," Dr. Eric Meslin, director of the Indiana University School of Medicine's Center for Bioethics, said.

He also said that collecting blood for one purpose and then storing it for another is not good public policy.

In 2013, Indiana changed its notification policy. Parents are now asked up front whether they will allow their newborn’s blood to be used for future research. If they say no, the samples will not be stored.

"Those are stored in the lab for six months, after which time we destroy them," said lab director Barb Lesko.

As for the 2.25 to 2.5 million samples from before last year, many of those may be unfit for research because of improper storage, WTHR reported. (Samples collected under the new policy are kept in locked freezers maintained at sub-zero temperatures.)

Now the state has decided to let the parents decide what’s to be done with their children’s samples.

"We are eager to hear what parents have to say," Bowman said. "We know there are some parents who would definitely like those samples destroyed. There are some parents who would like those samples kept. Determining how to exactly figure out which parents would want those samples kept and which ones would want them destroyed is presenting a challenge for us."

Parents with children born in Indiana can fill out consent forms - either allowing for their children’s samples to be used or destroyed - on the ISDH website.