Background Fatigue is one of the most common and disabling symptoms in multiple sclerosis (MS). The pathophysiology of fatigue is not fully understood. The aim of this study was to investigate a possible association between MS-related fatigue syndrome and disease modifying therapy. Methods A cross-sectional study in 343 consecutive patients with MS between Nov 2003 and Oct 2004 Was undertaken. Fatigue was assessed with the Fatigue Severity Scale (FSS). This analysis compromises patients with relapsing-remitting and secondary progressive MS. Three treatment groups (,,no therapy",,immunomodulation" and,,immunosuppression") were correlated with FSS by univariate analysis. We performed a stepwise backward logistic regression analysis to evaluate interaction with age, sex, course of disease, relapse rate, duration of disease or disability assessed by the Expanded Disability Status Scale (EDSS). Results We included 242 patients in this analysis. The prevalence of severe fatigue (FSS >= 5) was 51 %. In a multivariate logistic regression analysis controlled for age, course of disease, duration of disease and EDSS) there was no significant association between,,no treatment",,immunomodulation",,immunosuppression" and fatigue (OR 1.34, p=0.38 for immunosuppression and OR 0.95, p=0.85 for immunomodulation). Conclusions Although disease-modifying therapies in MS effectively reduce disease activity, they do not appear to have an significant effect on MS-related fatigue.