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Neglected tropical diseases are conditions directly associated to poverty and affect millions of people in tropical areas. Considering the necessity of pharmacokinetic and therapeutic drug monitoring studies to assess the disposition of agents clinically employed in the treatment of these diseases, especially in the involved population, this article will overview the current bioanalytical methods developed in the last 10 years, particularly those fully validated and using standard techniques, such as chromatographic procedures combined or not with mass spectrometry. The characteristics of each assay reported will be summarized and critically discussed. Furthermore, emphasis will also be given to the pros and cons in order to highlight the application of each method, especially in routine laboratories.