BackgroundMultiple Sclerosis (MS) is a demyelinating disease of central nervous system with an unknown etiology. Beta-Interferon is now widely used for treatment of MS which is believed to slow down the disease progression. This study was designed to compare the side-effects of Avonex and the Iranian 1-a Beta-Interferon, Cinnovex, which are biosimilars. MethodsThis was a clinical trial study in which fifty one MS patients were recruited from the neurology departments of Al-Zahra and Shariati hospitals in 2007. Twenty one patients were receiving Avonex and thirty patients were receiving Cinnovex. These patients were followed for 3 months to compare the side-effects of the drugs between two groups. FindingsThe most prevalent side effect observed was influenza like symptoms in all patients receiving Avonex and in 83.3% of patients receiving Cinnovex. There were no cases of seizure or diarrhea in any of groups. In this study, there were no significant differences between two groups in respect to experienced side-effects. ConclusionThis study with a short duration follow-up of 3 months demonstrated no significant differences between the two groups in case of experienced side-effects. Key words: CinnoVex, Avonex, side effects, treatment, Interferon beta 1-a, multiple sclerosis