One of the most important activities for quality assurance of malaria diagnosis is performance assessment. In Colombia, performance assessment of malaria microscopists has been done through the external performance assessment and indirect external performance assessment programs.To assess the performance of malaria microscopists of public reference laboratories using slide sets, and to describe the methodology used for this purpose.This was a retrospective study to evaluate the concordance of senior microscopists regarding parasite detection, species identification and parasite count based on the results of the assessment of competences using two sets, one comprising 40 slides, and another one with 17 slides.The concordance for parasite detection was 96.9% (95% CI: 96.0-97.5) and 88.7% (95% CI: 86.6-90.5) for species identification. The average percentage of concordant slides in the group evaluated was 89.7% (95% CI: 87.5-91.6).Most of the senior microscopists in Colombia were classified in the two top categories in the performance assessment using slide sets. The most common difficulty encountered was the identification of parasite species. The use of this tool to assess individual performance of microscopists in the evaluation of samples with different degrees of difficulty allows for characterizing the members of the malaria diagnosis network and strengthening the abilities of those who require it.