GENIRA [Gender in Rheumatoid Arthritis (RA)] is a comprehensive project aimed at studying gender differences in RA patients and how these differences impact on these patient outcomes. We are now reporting such data. Seventy RA patients of each gender were cross-sectionally evaluated following a preestablished protocol. Univariate and multivariate analyses focused in the different gender-associated comorbidity profiles and how they impact in the quality of life and disability of RA patients as assessed by the SF-36 and the Modified Health Assessment Questionnaire (M-HAQ), respectively. Both groups were comparable regarding their main demographic and clinical features. Different comorbidity profiles were found in both genders, with higher frequencies of diabetes mellitus, peptic ulcer, ischemic heart disease, smoking and chronic obstructive pulmonary disease among men and of depression and osteoporosis among women. The M-HAQ was lower in women than in men (0.89 ± 2.6 vs 0.22 ± 0.9, p = 0.04) as there were some sub-scales of the SF-36 [mental health (63.7 ± 22.0 vs 71.8 ± 21.1; p = 0.02), general health (41.3 ± 21.7 vs 50.0 ± 24.3; p = 0.02), physical functioning (PF) (57.7 ± 22.1 vs 67.3 ± 22.7; p = 0.01) and the physical summary component (PSC) (39.3 ± 8.9 vs 42.4 ± 9.3, p = 0.04)]. Multivariate analysis indicated the independent association between depression and osteoporosis rather than gender with the M-HAQ, PSC and PF and of only depression with the MH and GH. Women with RA present significantly worse disability and QOL outcomes than men; these differences can be explained by female gender-associated comorbidities such as depression and osteoporosis rather than gender per se.