Dr. Jones started his career at Johns Hopkins, initially working part-time while also working in the private clinic of the gynecologist Dr. Howard Kelly, who had pioneered radium therapy for cancer patients. Dr. Kelly was one of the so-called Big Four who had founded Johns Hopkins Hospital. In the 1950s, Dr. Jones collaborated on landmark studies with Dr. Richard Wesley TeLinde, proving that cervical cancer in situ — in which tumors have not invaded the cervix’s surface — was more dangerous than previously thought. They found that the tumors become deadly invasive cancers if left untreated.

Dr. Jones encountered Henrietta Lacks in 1951. The 30-year-old wife of a Baltimore steelworker, she showed up at Johns Hopkins Hospital — the only one near her that would treat blacks — complaining of a “knot” in her abdomen. Dr. Jones discovered a lump in her cervix and performed a biopsy, which led to a cancer diagnosis. Cancerous cervix cells that were subsequently removed from Ms. Lacks were the first to grow in culture.

The continued use of Ms. Lacks’ “immortal” cancer cell line, as biologists call it, led to breakthroughs in research on the polio vaccine, chemotherapy, cloning, gene mapping and in vitro fertilization. She died later, in 1951.

In her best-selling 2010 book, “The Immortal Life of Henrietta Lacks,” Rebecca Skloot reported that the cancerous cells had been removed from Ms. Lacks without the patient’s knowing it. (Oprah Winfrey’s production company has said it is adapting the book for an HBO film.) Dr. Jones, who did not perform the biopsy that yielded the immortal cells, maintained that Ms. Lacks had signed the permit “that all patients signed that was inclusive of doing everything we did.”

“There was no controversy,” he said. “That was something that was created later on.”

Dr. Jones began studying genital anomalies in the 1950s and became an authority in the field, collaborating with Dr. William Wallace Scott in writing the textbook “Hermaphroditism, Genital Anomalies and Related Endocrine Disorders,” published in 1958. He then became immersed in cancer research and did not return to it until the 1970s, when he began focusing on intersex teenagers, whose sexual anatomy does not fit typical definitions of female or male.

He began studying the chromosomes involved in the phenomenon at a lab he had started at Johns Hopkins. His clinical team of surgeons, endocrinologists and psychologists began treating patients with genital abnormalities from around the world.

The thinking at the time was that before the age of 18 months, children who underwent sex-change surgery would adapt psychologically to the sex in which they were reared. In other words, a baby could be switched from a boy to a girl or vice versa as long as the surgery was done early enough and the parents raised the child with, for example, gender-appropriate clothes and toys.