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Brilliant and hard-working, my younger colleague had just returned from delivering one of the main talks at a national medical meeting. All of us viewed the invitation to speak as an acknowledgment of her great potential, so when I asked her about the conference, I expected her to bubble over about the accolades she’d heard and the plum job offers she’d received from competing medical centers.

But she hardly smiled as she recounted her experiences.

Doctor and Patient Dr. Pauline Chen on medical care.

“During the question-and-answer session I kept falling back on phrases like ‘maybe,’ ‘perhaps’ and ‘I guess so,’ ” she said. Though she had the experience and data to rebut even the most aggressive or erroneous challenges from doctors in the audience, her tentative manner seemed to leave her vulnerable to doubts and even more questioning.

What’s more, she added, she had noticed that many of the other female speakers responded to their audiences as she had, with wavering and hesitant replies, while most of the men answered “with such confidence and bravado that we women looked pretty amateur in comparison.”

The experience had shaken my colleague’s quiet confidence. “I always thought the strength of my work was all that mattered in medicine,” she said. “Now I can’t help but wonder if other factors are involved.”

This was not the first time I had heard a colleague speculate on how her sex might affect the way others treated her professionally, but we all thought medicine was one of the few careers in which men and women working the same hours and producing comparable results in similar specialties would be paid and promoted equally. While some studies found income disparities between male and female doctors, researchers chalked up their findings to the fact that fewer women worked in higher-paying specialties and more men worked longer hours.

But a study published recently in The Journal of the American Medical Association reveals that medicine may not be so meritocratic after all.

Researchers analyzed the professional trajectories of almost 2,000 midcareer physician-researchers. Chosen because of their similarity to one another in professional interests, aptitude and ambition, the doctors in the study each had received a highly prestigious research grant early in their careers and worked not in private practice but in academic medical centers. The researchers examined a wide range of career factors, including the number of hours worked, professional achievements, leadership positions, marital status, parental status and salary.

As in some earlier studies, the researchers found a difference in income, with a male doctor’s annual salary averaging just over $200,000 and a female’s averaging about $168,000. And like previous researchers, they found that the female doctors tended to be in lower-paying specialties, have fewer publications, work fewer hours and hold fewer administrative leadership positions.

But when these researchers ran the numbers again, this time adjusting for differences in specialty, publications, academic rank, hours worked and leadership positions, they found that the expected average salary for women still fell behind that of their male colleagues. The male doctors made over $12,000 per year more than the women.

Calculated over the course of a 30-year career, the income gap based on sex alone amounted to over $350,000.

“We really didn’t expect to find such a substantial unexplained difference,” said Dr. Reshma Jagsi, lead author and an associate professor of radiation oncology at the University of Michigan. “In Michigan, that amount buys you a house, your kids’ education or a nice nest egg for retirement.”

There may be several reasons for this income difference. A previous study by a group of psychologists, for example, showed that when presented with identical résumés, one from a man and one from a woman, employers of both sexes were more likely to hire the man. A similar unconscious bias is likely to exist among doctors, influencing how much female physicians are paid and promoted. “It’s not like the medical centers or the department heads are evil,” Dr. Jagsi said. “The problem is that sometimes in medicine we think we are immune to these pervasive biases.”

Male and female doctors may also interact differently with their superiors when talking about payment and promotions. Women in other fields have been shown to negotiate less aggressively than their male peers. In medicine, that would mean women are less inclined to ask for more money and less likely to leverage offers from competing institutions or practices.

While the current study looks at only one small and homogeneous subset of physicians, the findings are probably applicable to many more doctors. “The men and women we studied were the go-getters,” Dr. Jagsi said. “You have to worry that if you see such disparities among this group, you will see at least the same, if not more, differences among other groups of physicians.”

Dr. Jagsi believes that greater transparency would decrease, and even eliminate, the income differences. Currently, it is difficult for most doctors to know if they are being paid fairly “since most institutions don’t have clear policies on how to determine salaries,” she noted. But standardizing the process of compensation and career advancement would make everyone involved more accountable for such decisions and “allow men and women to be paid as much as the work they are doing is worth,” she said.

“Society makes a huge investment in every medical trainee,” Dr. Jagsi said. “If we make that kind of investment, we need to ensure that compensation and advancement are fair.”

She added, “It comes down to a matter of basic fairness.”