It is unclear whether male and female physician researchers who perform similar work are currently paid equally.To determine whether salaries differ by gender in a relatively homogeneous cohort of physician researchers and, if so, to determine if these differences are explained by differences in specialization, productivity, or other factors.A US nationwide postal survey was sent in 2009-2010 to assess the salary and other characteristics of a relatively homogeneous population of physicians. From all 1853 recipients of National Institutes of Health (NIH) K08 and K23 awards in 2000-2003, we contacted the 1729 who were alive and for whom we could identify a mailing address.The survey achieved a 71% response rate. Eligibility for the present analysis was limited to the 800 physicians who continued to practice at US academic institutions and reported their current annual salary.A linear regression model of self-reported current annual salary was constructed considering the following characteristics: gender, age, race, marital status, parental status, additional graduate degree, academic rank, leadership position, specialty, institution type, region, institution NIH funding rank, change of institution since K award, K award type, K award funding institute, years since K award, grant funding, publications, work hours, and time spent in research.The mean salary within our cohort was $167,669 (95% CI, $158,417-$176,922) for women and $200,433 (95% CI, $194,249-$206,617) for men. Male gender was associated with higher salary (+$13,399; P = .001) even after adjustment in the final model for specialty, academic rank, leadership positions, publications, and research time. Peters-Belson analysis (use of coefficients derived from regression model for men applied to women) indicated that the expected mean salary for women, if they retained their other measured characteristics but their gender was male, would be $12,194 higher than observed.Gender differences in salary exist in this select, homogeneous cohort of mid-career academic physicians, even after adjustment for differences in specialty, institutional characteristics, academic productivity, academic rank, work hours, and other factors.