Inmates in correctional facilities have been shown to have poorer health than the general U.S. population, and there is some evidence that incarcerated women report higher morbidity than do men. The purpose of this study was to describe the health screening process that occurs at entrance into a county jail, and to identify excess morbidity, in particular among women. This is a cross-sectional study of inmates entering the San Joaquin County Jail from January 15 to March 15, 1998, screened for tuberculosis (TB) and self-reported presence of pulmonary or cardiovascular disease, sexually transmitted diseases, HIV/AIDS diagnosis, and drug or alcohol abuse. Of 1,871 inmates, 1,514 completed TB screening, 19.2% of whom had latent TB infection. Women were more likely to be released before skin test results could be read (odds ratio 1.65, 95% confidence interval 1.22-2.25). Women were more likely than men to report pulmonary disease (odds ratio 1.99, 95% confidence interval 1.17-3.39), cardiovascular disease (odds ratio 1.62, 95% confidence interval 1.03-2.55), and drug or alcohol abuse (odds ratio 2.02, 95% confidence interval 1.50-2.71), controlling for the influence of age. Both women and men reported more cardiovascular disease than age and gender-matched persons in the National Health Interview Survey of the U.S. population (standardized mortality ratio for jailed women under age 45: 2.00 [95% confidence interval 1.16-3.07] and for jailed men under age 45: 1.58 [95% confidence interval 1.23-1.97]). This study relied on a simple screening tool that may be useful for targeting further, more specific testing. Women, who may on average have less time in jail, need special efforts to complete screening.