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Background  The World Health Organization (WHO) recommended physician to population ratio is 23:10,000. Kenya has a physician to population ratio of 1.8:10,000 and is among 57 countries listed as having a serious shortage of health workers. Approximately 52 % of physicians work in urban areas, 6 % in rural and 42 % in peri-urban locations. This study explored factors influencing the choice of career specialization and location for practice among final year medical students by gender.    Methods  A descriptive cross-sectional study was carried out on final year students in 2013 at the University of Nairobi’s, School of Medicine in Kenya. Sample size was calculated at 156 students for simple random sampling. Data collected using a pre-tested self-administered questionnaire included socio-demographic characteristics of the population, first and second choices for specialization. Outcome variables collected were factors affecting choice of specialty and location for practice. Bivariate analysis by gender was carried out between the listed factors and outcome variables with calculation of odds ratios and chi-square statistics at an alpha level of significance of 0.05. Factors included in a binomial logistic regression model were analysed to score the independent categorical variables affecting choice of specialty and location of practice.    Results  Internal medicine, Surgery, Obstetrics/Gynaecology and Paediatrics accounted for 58.7 % of all choices of specialization. Female students were less likely to select Obs/Gyn (OR 0.41, 95 % CI =0.17-0.99) and Surgery (OR 0.33, 95 % CI = 0.13-0.86) but eight times more likely to select Paediatrics (OR 8.67, 95 % CI = 1.91-39.30). Surgery was primarily selected because of the ‘perceived prestige of the specialty’ (OR 4.3 95 % CI = 1.35-14.1). Paediatrics was selected due to ‘Ease of raising a family’ (OR 4.08 95 % CI = 1.08-15.4). Rural origin increased the odds of practicing in a rural area (OR 2.5, 95 % CI = 1.04-6.04). Training abroad was more likely to result in preference for working abroad (OR 9.27 95 % CI = 2.1-41.9).    Conclusions  The 4 core specialties predominate as career preferences. Females are more likely to select career choices due to ‘ease of raising a family’. Rural origin of students was found to be the most important factor for retention of rural health workforce. This data can be used to design prospective cohort studies in an effort to understand the dynamic influence that governments, educational institutions, work environments, family and friends exert on medical students’ careers.    Electronic supplementary material  The online version of this article (doi:10.1186/s12909-016-0528-1) contains supplementary material, which is available to authorized users.

Career preferences of final year medical students at a medical school in Kenya–A cross sectional study