BACKGROUND: Humoral autoimmunity in patients with multiple sclerosis is often asymptomatic and transient during interferon therapy. OBJECTIVE: To analyze the frequency of positivity to autoantibodies in multiple sclerosis patients, and to clarify whether it is modified by immunomodulating therapy. DESIGN: A retrospective study. TIME AND SETTING: The study was performed at the Multiple Sclerosis Center, Department of Neurosciences, Salo Hospital, Italy, between 2005 and 2007. ARTICIPANTS: A total of 169 multiple sclerosis patients were included, 57 males and 112 females. Individuals were mainly outpatients and were usually tested yearly for autoantibodies. Patients with revious immunological diseases were excluded from statistical evaluation. METHODS: The frequency of positivity was calculated in patients grouped for gender, multiple sclerosis clinical parameters, magnetic resonance imaging features and disease modifying therapy. A total of 113 patients were treated with beta interferons. MAIN OUTCOME MEASURES: Frequency of positivity to any autoantibody. Prevalences and incidences were calculated. RESULTS: The overall prevalence of autoantibodies within 3 years was 47.3%. In multiple sclerosis atients who were untreated or treated with drugs other than interferons, the prevalence was higher, and greater positivity to autoantibodies was seen in patients treated with interferons [odds ratio (95% confidence interval), 2.87 (1.5 - 5.2), P < 0.05 - 0.01 ]. Multiple regression analysis showed a significant association of the positivity to autoantibodies with interferon therapy, rather than gender, relapse or magnetic resonance imaging. CONCLUSION: Interferon therapy is associated with significantly higher frequency of autoantibodies in patients with multiple sclerosis. The differences among the therapies are not influenced by other variables such as gender or clinical patt.