Several studies highlight the role of physicians in determining cervical and breast cancer screening rates, and some urban studies report higher screening rates by female physicians. Rural women in North America remain underscreened for breast and cervical cancers. This survey was conducted to determine if there were significant gender differences in practices and perceptions of barriers to breast and cervical cancer screening among rural family physicians in Ontario, Canada. One hundred ninety-one family physicians (response rate 53.1%) who practiced in rural areas, small towns, or small cities completed a mail questionnaire. The physicians' mean age was 44.4 years (SD 9.9), and mean number of years in practice was 16.6 years (SD 10.3). Over 90% of physicians reported that they were very likely to conduct a Pap test and clinical breast examination (CBE) during a periodic health examination, and they had high levels of confidence and comfort in performing these procedures. Male (68%) and female (32%) physicians were similar in their likelihood to conduct screening, levels of confidence and comfort, and knowledge of breast and cervical cancer screening guidelines. However, the self-reported screening rates for Pap tests and CBE performed during last year were higher for female than male physicians (p < 0.01). Male physicians reported they were asked more frequently by patients for a referral to another physician to perform Pap tests and CBE (p < 0.001). Also, male physicians perceived patients' embarrassment as a stronger barrier to performing Pap tests (p < 0.05) and CBE (p < 0.01) than female physicians. No gender differences were observed in screening rates or related barriers to mammography referrals. These findings suggest that physicians' gender plays a role in sex-sensitive examination, such as Pap tests and CBE. There is a need to facilitate physician-patient interactions for sex-sensitive cancer screening examinations by health education initiatives targeting male physicians and women themselves. The feasibility of providing sex-sensitive cancer screening examinations by a same-sex health provider should also be explored.