Background: Skin abscesses are a source of considerable physical suffering, anxiety, morbidity/mortality, and health care costs for injection drug users (IDUs). Previous studies have found that the prevalence of abscesses is higher among female IDUs than male IDUs. However, the research exploring this gender disparity and gender-specific correlates with abscesses is sparse. The purpose of this study was to determine if the prevalence of abscesses was higher among female IDUs than male IDUs in San Diego and explore gender-specific correlates with abscesses among this population. Methods: This analysis uses the STAHR I data collected by researchers at the University of California at San Diego (UCSD). Between May 2009 and June 2010, the researchers conducted a cross-sectional survey among injection drug users in San Diego who were between the ages of 18 and 40. Of the 566 participants in the STAHR I study, 552 were eligible for this study. Results: Among 552 participants, 399 were male and 153 were female. Of male participant, 7.0% reported having an abscess at the time of the study compared to 15.7% of female participants. Among 18-40 year old injection drug users in San Diego, abscess prevalence was higher for females than males (OR=2.47; CI: 1.38-4.44). Different variables were associated with having a current abscess for males and females in bivariate analysis. In bivariate analysis, the variables associated with having a current abscess in females were injecting heroin by itself (p<0.0001), times injecting in previous three months (p=0.004), using a syringe exchange program (p=0.0048), receiving income from sex work (p=0.007), number of times using a syringe before discarding it (p=0.012), number of years injecting (p=0.032), and injecting heroin and cocaine together, speedball (p=0.0283). In bivariate analysis, the variables associated with having an abscess in males were using a syringe exchange program (p=0.002), number of times injecting in previous three months (p=0.0196), number of times injecting with other people (p=0.028), and injecting in their own home (p=0.032). Receiving income from trading sex for money in the previous six months was independently associated with having an abscess in women (OR=14.3; 95% CI: 2.27-90.22) but not in men (OR=1.98; 95% CI: 0.34-11.56). Injecting speedballs in the previous three months was also not independently associated with having a current abscess in men (OR=1.32, 95% CI: 0.38-4.63). Conclusions: The gender disparity in the prevalence and correlates of skin abscesses among IDUs indicates that abscess prevention programs would benefit from gender-specific program planning.