The aim of this study was to evaluate the long-term adverse effect (AE) profile of azathioprine (AZA) plus methylprednisolone combined immunosuppressive treatment in myasthenia gravis (MG) in a larger patient cohort. A prospective, open, observational study was conducted on 163 MG patients treated with combined immunosuppressive medication for a mean duration of 35.5 months (range 9-79 months). During the treatment course, AEs occurred in 61.4% of patients; 18% of these patients developed both steroid- and AZA-related AE, 15% had purely AZA-related AE and 67% had steroid-associated AEs. Severe AEs were encountered in only 6.7% of patients in whom treatment had to be discontinued. The clinical severity of MG at the start of the immunosuppressive treatment was positively correlated with the frequency and severity of AEs during the treatment, and patients with severe MG were found to be at higher risk of developing AEs during the combined immunosuppressive treatment. Combined immunosuppressive treatment of MG patients is well tolerated, and severe AEs requiring treatment cessation are rare. The incidence of steroid-related AEs is high during long-time therapy which underlines the importance of its combination with AZA. The probability of developing AEs seems to correlate with the severity of MG at the beginning of the treatment.