Objective: To assess how physical limitations relate to self-rated health among family medicine patients after adjustment for severity of illness. Design: A telephone survey of family medicine patients, linked with medical record information. Setting: A large family medicine department in Rochester, Minnesota, USA. Subjects: Self-ratings of health were linked to medical records for 804 adult patients. Results: Adjusting for severity and other confounders using multiple logistic regression analysis revealed that having physical limitations was inversely and independently related to good self-rated health (adjusted odds ratio = 0.20, P<0.001). Odds ratios also were lower for high severity of illness (adjusted odds = 0.43). Morbidly obese patients and patients older than 65 years of age also had reduced odds of good self-rated health. Conclusions: In our sample of family medicine patients, part of the disparity in health status experienced by people with physical limitations is attributable to greater severity of illness, age and obesity.