Each year, evidence-based clinical guidelines gain more space in the health professionals' practice and in services organization. Due to the scarcity of scientific publications focused on diseases of poverty, the development of well-founded clinical guidelines becomes more and more important. In view of that, this paper aims to evaluate the quality of Brazilian guidelines for those diseases. The AGREE II method was used to evaluate 16 guidelines for poverty-related diseases (PRD) and 16 guidelines for global diseases whose treatment require high-cost technologies (HCD), with the ultimate aim of comparing the results. It was found that, in general, the guideline development quality standard is higher for the HCD guidelines than for the PRD guidelines, with emphasis on the "rigour of development" (48% and 7%) and "editorial independence" (43% and 1%) domains, respectively, which had the greatest discrepancies. The HCD guidelines showed results close to or above international averages, whereas the PRD guidelines showed lower results in the 6 domains evaluated. It can be concluded that clinical protocol development priorities need some redirecting in order to qualify the guidelines that define the healthcare organization and the care of vulnerable populations.