Specialty distribution in Kenya continues to exhibit gender disparities despite the increasing number of female medical students graduating each year. This study aimed at assessing specialty preferences and factors influencing these choices among male and female medical students in Kenya. Four hundred and fifty medical students, from first to fifth year of study at the University of Nairobi, were each issued a self-administered questionnaire designed to assess their specialty preferences and factors influencing these choices. The specialty preferences were compared with the actual distribution of specialists in Kenya. Data collected were analyzed using Statistical Package for Social Sciences. Three hundred and eighty five (85.6%) questionnaires were completed. Surgery had the highest preference rate followed by pediatrics, internal medicine and obstetrics and gynecology. Significantly more males preferred surgery than females who mainly selected pediatrics (p<0.001). There was an increased likelihood of female students choosing controllable lifestyle specialties. These preferences mirrored the actual distribution of specialists in Kenya. Male students significantly considered prestige in a specialty (p=0.006), while their female counterparts mostly considered ease of raising a family and gender distribution in the specialty (p<0.001). Gender-based similarities and differences exist in factors influencing specialty preferences among Kenyan medical students. These factors may explain the observed specialist doctor distribution in the country.