OBJECTIVES: This study aimed to investigate the patterns of medication treatment among patients with Multiple Sclerosis (MS) treated in the Brazilian Public Healthcare System (BPHS) and examine possible temporal and spatial trends in those patterns. METHODS: The study was a longitudinal analysis of Brazilian MS pharmacy claims as reported in the Brazilian Ambulatory Information System Database for the period 2006-2009. Five different drugs currently recommended at BPHS MS guidelines were included in the analysis (Glatiramer 20mg, Betainterferon 22mcg, Betainterferon 44mcg, Betainterferon 30mcg, Betainterferon 300mcg) and the proportion of patients receiving each drug was calculated using defined daily doses. Changes in this distribution over time across all 27 Brazilian states were analyzed. RESULTS: The estimated yearly number of MS patients treated within the BPHS was 3,569, 4,894, 5,800, and 6,099 from 2006 to 2009. The probability of use of Glatiramer 20mg increased from 9.5% in 2006 to 20.1% in 2007, maintaining similar proportions in the following years (20.7% and 21.28%). The lower proportion of treated patients was observed for Betainterferon 22mcg, with a constant decrement from 2006 (17.26%) to 2009 (11.39%). The other three available Betainterferon formulations represented stable distribution of 20-25% each across all years with a slightly greater probability of use of the 30mcg intramuscular formulation (administered weekly). Between-states differences were also analyzed and revealed important spatial discrepancies. For instance, the probability of use of Glatiramer in 2009 was 32% in Bahia (Northeast Region) and 13% in Santa Catarina (South Region) and the proportion of MS patients taking Betainterferon 30mcg was 36% in Rio Grande do Sul (South Region) and 15% in Bahia. CONCLUSIONS: Although a proportional distribution of Glatiramer and Betainterferon formulations is coherent with the BPHS guideline which stated that their efficacy should be considered similar, significant between-states discrepancies in terms of treatment patterns were identified.