OBJECTIVES To evaluate the impact of the patient's adherence to national guideline in the treatment costs. METHODS A one-year (January 2007 to December 2007) retrospective database search was conducted to identify medication used, costs, patient adherence and provision. The source of data was the Ministry of Health public available database, called DATASUS. The study were conduct in four steps: 1) Determine the medicines codes in the public list; 2) Establish the relationships among drugs and patients usage; 3) Analyze adherence pattern at country level, based on medication consumption; and 4) Estimate the impact of adherence in the treatment costs. RESULTS Medication for MS was responsible by 12.9% of high cost medication supplied by Public Sector in Brazil. During the period of analysis an average of 34.4% of patients adhere to treatment from 10 to 12 months. Patients treated were distributed among therapeutics alternative as follow: 60.66% to interferon-1a (two brands), 20.5% to interferon-1b and 18.85 to glatiramer acetate. It was possible to detect an increase in drugs association. We found the following adherence per treatment: 36.9% to glatiramer acetate, 33.67% to interferon-1a (two brands) and 32.3% to interferon-1b. Due to these levels of adherence the annual costs per patient treated was USD 27,824 to glatiramer acetate, US$42,151 to interferon-1a (two brands) and US$34,038 to interferon-1b. Total treatment costs was higher than USD92 millions per year (R$2.5 / USD1.0), the distribution of costs begins to diverge from patients distribution due to combination therapy. CONCLUSIONS National guidelines standardize care, but the analysis of treatment patterns points to low treatment adherence. Due to actual levels of adherence the costs per patient treated was three times higher than the expected. Actions taken to change these levels will have a considerable impact to reduce the cost per patient treated.