OBJECTIVES: To estimate the prevalence of drug-treated MS within the Brazilian public healthcare system (BPHS) and compare it with published prevalence rates. METHODS: A previously described method to estimate the prevalence of diseases treated with drugs that are specific to them and must be taken continuously was employed. The total amount of MS drugs (Glatiramer 20mg, Betainterferon 22mcg, Betainterferon 44mcg, Betainterferon 30mcg, Betainterferon 300mcg) dispensed from 2006 to 2009 was obtained from the Ambulatory Information Database and the daily doses defined by BPHS MS guidelines were used to convert it in drug-treated cases. The drug-treated prevalence was compared with rates achieved through conventional cross-sectional studies (4.27-15/100,000). Complementary analysis was performed using Brazilian private health plans coverage data. RESULTS: The estimated drug-treated prevalent cases within the BPHS were 3,569 in 2006 with a constant increasing until 2009 when reached 6,099. Drug-treated prevalence rates (per 100,000) were 1.93, 2.63, 3.08, and 3.21 in 2006, 2007, 2008, and 2009, respectively. MS prevalent cases in the BPHS were estimated as ranging from 7,838 in 2006 to 8,113 in 2009 using the 4.27/100,000 rate and from 27,533 in 2006 to 28,499 in 2009 using the 15/100,000 rate. The prevalence of MS estimated from drug consumption data was found to be 24.8-78.6% lower than that estimated from cross-sectional studies. Even when private health plans coverage (≈20%) was considered, the difference remained substantial between drug-treated and BPHS prevalent cases (total prevalent cases minus those supposed to have private coverage). In 2009, this difference ranges from 310 (BPHS cases minus drug-treated cases) to 22,399 (prevalent cases using 15/100,000 minus drug-treated). CONCLUSIONS: These findings raise important questions about barriers to access to MS treatment, undertreatment and/or underdiagnosis of MS and the reliability of the available prevalence rates for use in projecting eligible population and performing budget impact analysis.