Multiple sclerosis is associated with significant impacts on both the patient's quality of life and the healthcare payer's budget. The therapy of multiple sclerosis is mainly implemented by the administration of expensive immunomodulatory drugs. The aim of this study is to evaluate the cost-effectiveness of two approaches in the treatment of multiple sclerosis in adult patients, comparing SC glatiramer acetate 40 mg and SC interferon beta-1a 44 mu g from the perspective of a healthcare payer. The cost-effectiveness analysis was calculated based on effects identified by multicriteria decision making and direct costs from a healthcare payer perspective. Validation of the results was ensured by one-way sensitivity analysis. For the evaluated intervention SC glatiramer acetate 40 mg, the costs are CZK 176,933 and the effects are 0.24. For SC interferon beta-1a 44 mu g, the costs are CZK 175,863 and the effects are 0.76. The resulting ICER was evaluated at -2,229 CZK, suggesting cost ineffectiveness of SC glatiramer acetate 40 mg compared with the comparator SC interferon beta-1a 44 mu g.