BackgroundThe increasing proportion of women in the medical profession is a worldwide phenomenon often called the “feminization of medicine.” However, it is understudied in low and middle-income countries, particularly in Latin America.MethodsUsing a qualitative, descriptive design, we explored the influence of gender and other factors on physician career decision-making and experiences, including medical specialty and public vs. private practice, in Quito, Ecuador, through in-depth, semi-structured interviews (n = 31) in 2014. Theoretical sampling was used to obtain approximately equal numbers of women and men and a range of medical specialties and practice settings; data saturation was used to determine sample size. Transcripts were analyzed using content coding procedures to mark quotations related to major topics and sub-themes included in the interview guide and inductive (grounded theory) approaches to identify new themes and sub-themes.ResultsGendered norms regarding women’s primary role in childrearing, along with social class or economic resources, strongly influenced physicians’ choice of medical specialty and practice settings. Women physicians, especially surgeons, have had to “pay the price” socially, often remaining single and/or childless, or ending up divorced; in addition, both women and men face limited opportunities for medical residency training in Ecuador, thus specialty is determined by economic resources and “opportunity.” Women physicians often experience discrimination from patients, nurses, and, sometimes, other physicians, which has limited their mobility and ability to operate independently and in the private sector. The public sector, where patients cannot “choose” their doctors, offers women more opportunities for professional success and advancement, and the regular hours enable organizing work and family responsibilities. However, the public sector has generally much less flexibility than the private sector, making it more difficult to balance work and family responsibilities.ConclusionWomen may outnumber men in medicine in Ecuador and across many parts of the world, but a number of structural issues-economic, social, and cultural-must be addressed for women to establish themselves in a wide variety of medical specialties and practice settings and for countries to realize the benefit of the investments being made to train and employ them.Electronic supplementary materialThe online version of this article (doi:10.1186/s12913-016-1917-1) contains supplementary material, which is available to authorized users.