OBJECTIVE: To investigate the association between two indices of obesity, BMI and waist-to-hip ratio (WHR), and self-reported physical and mental functional health. RESEARCH METHODS AND PROCEDURES: We examined the relationship between obesity indices and self-reported physical and mental functional health measured by the Anglicized version of the Short-Form 36-item questionnaire in a population-based cross sectional study of 16,806 men and women 40 to 79 years old living in the general community in Norfolk, United Kingdom. RESULTS: Higher BMI and WHR were both independently associated with poorer self-reported physical functional health in men and women. The effect of BMI was greater in women compared with men, and the effect of WHR was greater in men compared with women, for poor physical functional health. Higher WHR but not BMI was associated with lower mental functional health in men and women. DISCUSSION: High BMI and WHR seem to be adversely related to self-perceived functional health in both men and women, although their relative impacts seem to differ by sex. Our findings also highlight the importance of using WHR in addition to BMI in assessing the impact of obesity on health outcome.