THE FIRST THING MOST NEW MOTHERS HEAR, even before the cry of their newborn child, is a physician saying “It’s a boy” or “It’s a girl.” But in about one out of 2,000 deliveries, that determination can be hard to make.

Some babies are born with sex organs or genetic features that are not typical for their biological sex. They are dubbed “intersex,” a term that covers more than 30 conditions clinically known as disorders of sex development (DSD) or, sometimes, differences of sex development. Physicians have generally performed genital “normalizing” procedures on intersex children during their first year, bringing their bodies—at least cosmetically—in line with one sex or the other.

But these surgeries have physical and psychological costs. Many intersex people embark on a life of hormone replacement therapy, and they may have physical scars that can impair genital intercourse or ensure that they will never be able to have biological children. Studies of adults who had such surgery as infants show mixed satisfaction with the results, and some recount harrowing experiences, particularly when they did not grow up to identify as the sex that their surgery assigned them.

It may be time to rethink the treatment of intersex children, says Joshua Safer, medical director of the Center for Transgender Medicine and Surgery at Boston Medical Center. “These surgeries were the norm when we thought that gender identity could be manipulated,” he says, “but there’s a growing recognition that gender is substantially a biological phenomenon. It’s essentially hardwired.” Patients, given time to grow up a little, will be in a better position than their doctors to know which sex they are.

Some advocates have called for curtailing these surgeries, if not prohibiting them outright. A 2013 report by the United Nations’ Commission on Human Rights called for an end to “genital normalizing” of intersex children. A year later, several U.N. agencies, including the World Health Organization and UNICEF, condemned unnecessary surgery on intersex children without their consent, with Malta in 2015 becoming the first country to outlaw the procedures.

Momentum is also growing in the United States, where the State Department, major LGBTQ rights organizations and three former U.S. surgeons general also supported calls for a ban over recent years. This past July, Human Rights Watch and InterACT, a group advocating for intersex youth, coordinated a major push that asked federal legislators, regulators and medical societies to delay these procedures, if medically possible, until patients can participate in the decision.

The groups issued a 186-page research report containing interviews with dozens of specialists and intersex adults. “The results of the surgeries are often catastrophic, the supposed benefits are largely unproven, and there are generally no urgent health considerations at stake,” says Kyle Knight, the report’s author. The document also decried a lack of standards for care of intersex patients and wide variation in treatment protocols.

“There is room for improvement,” says David Sandberg, a pediatric psychologist and professor at the University of Michigan Medical School. Sandberg is a principal investigator for the DSD-Translational Research Network, a project funded by the National Institutes of Health to expand research into disorders of sex development and to establish best practices for diagnosis and treatment. But Sandberg is critical of the HRW-InterACT report’s methodology and some of its conclusions. The researchers received input from 21 out of the 218 contacted health care practitioners, a number he considers insufficient. And the spectrum of conditions is too broad for blanket statements about care, he says.

Other specialists agree. “The report is spearheaded by activist groups, which makes it problematic,” says Karen Lin Su, a pediatric endocrinologist at Weill Cornell Medicine in New York City. Su is particularly concerned about limiting the options available to physicians and patients. “Treatment should be approached on a case-by-case basis,” Su says. “Some of these conditions can be life-threatening without surgery, and decisions about what to do should be made by the medical team and the family, not the political arena.”

Boston Medical Center’s Safer hopes that medical societies can move quickly tomprove guidelines about when and how these surgeries should happen. “We need them to step up and give us detailed standards of care,” he says.

The American Medical Association, the largest organization of U.S. physicians, doesn’t currently have a policy addressing treatment for intersex babies. But the group is considering a recommendation to defer intersex surgery on infants, except for life-threatening conditions, until the child is able to participate in the decision-making. The 66,000-member American Academy of Pediatrics has said it is conducting an ongoing evaluation of treatments, and it has urged physicians to be transparent with patients’ families about the potential risks and benefits.

In the meantime, a lawsuit—the first of its kind—was filed in South Carolina against a hospital system and the state’s Department of Social Services by an intersex patient. He had been in their care as a baby and underwent surgery that assigned his gender as female, while he was too young to give informed consent. The patient now identifies as male. The case was settled out of court last summer.