The number of clinical guidelines is increasing worldwide, while there are concerns regarding their quality. In 2000, the Brazilian Ministry of Health began its process of creating clinical guidelines, called Clinical Protocols and Therapeutic Guidelines (PCDT). The goal of this study was to assess the quality of Brazilian guidelines approved since 2009 using the AGREE II instrument (Appraisal of Guidelines for Research and Evaluation). We identified 59 PCDT from 2009 to 2012, of which eight were randomly selected and evaluated by three independent evaluators. For the item "recommends the guidelines", two evaluators recommended the use of all eight, but with modifications, and one did not recommend any to the guidelines. Regarding the item "global quality of the guidelines" (varying from 1 to 7), the mean was 4.25 (SD = 0.46). The results showed the need for adjustments in the PCDT in relation to AGREE II domains. However, due to the instrument's limitations, further studies are needed, including the quality of evidence used in the PCDT.