Background: Neglected Tropical Diseases are a group of infectious diseases that receive little or no research fund and treatment investment around the world. These diseases, added to other infectious diseases, such as tuberculosis, malaria and toxoplasmosis, represent an important cause of morbidity and mortality in low-income countries. Brazil has a significant number of people affected by these diseases but had not yet developed evidence-based guidelines with this focus.

Objectives: To describe the prioritisation and development process conducted by the Brazilian Ministry of Health for the development of evidence-based clinical guidelines for infectious and neglected tropical diseases.

Methods:Descriptive case study

Results:The process of developing guidelines for infectious diseases encounters difficulties in the use of systematic methods for elaboration and a need for less time for the document completion. Submission of the proposed scope to online public consultation has shown to be an important tool to incorporate society's demands on guidelines development process. At the end of the process, with the publication of these guidelines, it is expected to standardise methodologies and offer better treatment options for patients with neglected diseases and infectious diseases in Brazil.

Conclusions:The process of developing guidelines for infectious diseases encounters difficulties in the use of systematic methods for elaboration and a need for less time for the document completion. Submission of the proposed scope to online public consultation has shown to be an important tool to incorporate society's demands on guidelines development process. At the end of the process, with the publication of these guidelines, it is expected to standardise methodologies and offer better treatment options for patients with neglected diseases and infectious diseases in Brazil.