OBJECTIVES: Since 2012, the Ministry of Health, specifically the National Commission for Health Technology Incorporation (CONITEC) produces the guidelines for diagnosis and treatment of various diseases treated within the Brazilian public health system (SUS). We aimed to analyze if these clinical guidelines are in line with AGREE II (The Appraisal of Guidelines for Research and Evaluation Instrument) criteria. METHODS: All the guidelines produced since 2012, except the oncology guidelines, were confronted with the AGREE II criteria. This tool has 23 items distributed in 6 domains: (1) Scope and Purpose, (2) Stakeholder Involvement, (3) Rigor of Development, (4) Clarity of Presentation, (5) Applicability, (6) Editorial Independence. Each item could be classified as in line (YES), not in line (NO), PARTIALLY in line and NOT APPLICABLE to AGREE II criteria. The results were measured in percentage and grouped by type of response and domain. RESULTS: Four documents containing health policies to specific populations were excluded. We analyzed 54 clinical practice guidelines. The AGREE II 23 items were analyzed for each protocol generating 1,242 responses. 50.4% of the responses were YES, 40.7% were NO, 8.6% PARTIALLY, and <1% of the answers were NOT APPLICABLE. Regarding the instrument domains, the largest adequacy ratio was found in the domain 1, with 74.0% YES. The smallest adequacy ratio occurred in the domain 5, with only 25.9% YES. Of note, domains 2 and 6, only achieved 32.7% and 31.4% YES responses, respectively. CONCLUSIONS: The clinical practice guidelines produced by the Brazilian Ministry of Health achieved median agreement (50.4% YES) with AGREE II quality criteria. In light of the AGREE II quality criteria the guidelines still have to improve although we could observe changes in the drafting process leading to a better methodological quality when we analyzed the guidelines in chronological order.