Background: Physicians’ inadequate involvement in sexual risk assessment has the potential to miss many asymptomatic cases. The present study was conducted to explore sexual risk assessment by physicians in clinical practice and to identify barriers in eliciting sexual histories from patients. Methods: A stratified random sample of 15% of general practitioners (GP) from New South Wales was surveyed to assess their management of sexually transmissible infections (STI). In total, 409 GP participated in the survey with a response rate of 45.4%. Results: Although nearly 70% of GP regularly elicited a sexual history from commercial sex workers whose presenting complaint was not an STI, this history taking was much lower (<10%) among GP for patients who were young or heterosexual. About 23% never took a sexual history from Indigenous patients and 19% never elicited this history from lesbian patients. Lack of time was the most commonly cited barrier in sexual history taking (55%), followed by a concern that patients might feel uncomfortable if a sexual history was taken (49%). Other constraints were presence of another person (39%) and physician’s embarrassment (15%). About 19% of GP indicated that further training in sexual history taking could improve their practice. Conclusions: The present study identifies inconsistent involvement by GP in taking sexual histories, which can result in missed opportunities for early detection of many STI. Options for overcoming barriers to taking sexual histories by GP are discussed.