Homeless individuals experience high rates of morbidity and mortality, yet many homeless studies include small percentages of female participants. We therefore sought to determine correlates of homelessness separately for men and women in a sample of individuals visiting free food programs. Between August 2003 and April 2004, 324 individuals were recruited from San Francisco free food programs and interviewed regarding housing, sociodemographics, health, drug use, sex trade, and incarceration. Over one-half of women and almost three-fourths of men reported homelessness in the prior year. Among women, white race, younger age, not living with minor children, engaging in sex trade and recent incarceration were strongly associated with homelessness; however, only incarceration maintained the strong association in adjusted analysis (OR = 7.16, CI = 3.83-13.4). Among men, heavy alcohol use, drug use, years spent living in San Francisco and monthly income were strongly associated with homelessness; however, only years living in San Francisco (OR = 0.28, CI = 0.19-0.42) and monthly income maintained strong association in adjusted analysis (OR = 0.27, CI = 0.13-0.57). Housing patterns and the strongest correlates of homelessness among individuals visiting free food programs differ by sex. These results suggest the need to characterize homelessness and develop effective homeless interventions separately for men and women.