There is a rising incidence of sexually transmitted infections (STIs) in Bahrain. This study aimed to determine physician practices with regard to sexual and reproductive health in women in the primary care setting in Bahrain, and to ascertain if physician gender affected these. The study included all eligible Ministry of Health family physicians (217) in 2006 and data were collected by a self-completed questionnaire; the response rate was 90.3%. Over half (58%) of the responding physicians were female. Male physicians did not undertake gynaecological examinations nor carry out STI screening procedures for asymptomatic women, and rates for women physicians were low (28.9% and 11.4% respectively). As regards to identification of and counselling for sexual health and STI risk factors, there were no differences between male and female physicians in addressing these issues with less than 25% doing so. All physicians would benefit from continuing education in the area of sexual medicine regardless of their gender.