BACKGROUND: Gender appears to play a role in incidence and disease course of multiple sclerosis (MS). OBJECTIVE: The objective was to determine whether male and female patients with MS respond differently to interferon-beta treatment in terms of reduction in relapse rates. METHODS: We included all 2033 patients with relapsing-remitting MS who started treatment with interferon-beta from 1996 to 2003, identified from the Danish Multiple Sclerosis Treatment Register. We defined neutralizing antibody (NAb)-positive and NAb-negative periods in the single patient by the results of the NAb tests. Patients served as their own controls, and relapse rates were compared between NAb-negative and NAb-positive periods. RESULTS: NAbs significantly abrogated the interferon-beta treatment efficacy in both genders. The all-over women:men relapse rate ratio irrespective of NAb status was 1.47 (95%CI; 1.28-1.68). In a generalized linear Poisson models analysis with relapse counts as response variable, the main effects NAbs, sex, age at treatment start and number of relapses in 2 years before treatment start were strongly significant, but the effect of NAbs on relapse rates did not differ significantly between men and women. CONCLUSION: As NAbs influenced the on-treatment relapse rates strongly in both sexes but without statistical significant difference, there is no indication of different effects of interferon-beta in men or women.