OBJECTIVES: To compare outcomes of multiple sclerosis (MS) patients treated with either glatiramer acetate (GA) or interferon beta 1-b (IFN-β-1b) for subcutaneous administration. METHODS: Data were obtained from i3’s Lab Rx Database from July 2001 to June 2006.  We established an “intent-to-treat” (ITT) cohort (N=842) of patients diagnosed with MS who began therapy on either GA or IFN-β-1b and had continuous insurance coverage from 6 months before to 24 months after the date when they began taking the medication.  We also created a “continuous use” (CU) cohort (n=418) of individuals who, in addition to the criteria above, used either GA or IFN-β-1b within 28 days of the end of the two year post-period. Using multivariate regressions, we examined both the two-year total direct medical costs and the likelihood of relapse associated with the use of each of these MS medications. We defined relapse as either being hospitalized with a diagnosis of MS or being diagnosed with MS during an outpatient visit and then prescribed steroids within a 7-day period.  All regression analyses evaluated a wide range of factors that may affect outcomes.RESULTS: :  In the ITT cohort, compared to those who started therapy with IFN-β-1b, patients who started therapy on GA had a significantly lower two-year risk of relapse (13.54% v 5.31%; P=0.0006).  In the CU cohort, compared to those who used IFN-β-1b, patients who used GA also had a significantly lower two-year risk of relapse (10.919% v 2.09%; P=0.0018) and significantly lower total medical costs ($53,185 v $48,130; P=0.0345).CONCLUSIONS: Results from this study indicate that, compared to the use of IFN-β-1b,  GA use is associated with significantly lower probability of relapse.  Additionally, when comparing continuous users of GA or IFN beta-1b, there were significantly lower two-year total direct medical costs associated with GA use.