Comparative effectiveness research (CER) has emerged as a priority for outlining the advantages and disadvantages of disease-modifying therapies (DMTs) for multiple sclerosis (MS). CER can provide physicians with valuable information to assist them in selecting the most appropriate therapeutics for their patients with MS. For payers, data from CER could inform decisions regarding the level of coverage for current and developing MS therapeutics, and drive the use of the most effective treatments for patients with MS. The base of CER data for DMTs has been expanding, and findings from a number of CER studies for currently available DMTs have been published, while further CER studies are planned to evaluate currently available and new DMTs or DMTs in development. While CER can be used to guide DMT selection for physicians and payers, the safety and tolerability of these treatments must be considered as well. Other emerging factors (eg, biomarkers and patient-specific factors) may also serve as important determinants of DMT choice in the future.