Objectives. To assess the competency of microscopists for malaria diagnosis using standardized slide sets in the Peruvian Amazon. Material and methods. Cross-sectional study carried out in 122 first level health facilities of the Peruvian Amazon, between July and September 2007. Within the frame of the project "Control Malaria in the border areas of the Andean Region: A community approach" (PAMAFRO), we evaluated the malaria diagnosis performance in 68 microscopists without expertise (< 1 year of expertise) and 76 microscopists with expertise (> 1 year) using standardized sets of 20 blood smear slides according to the World Health Organization (WHO) recommendations. A correct diagnosis (correct species identification) was defined as "agreement", a microscopist was qualified as an "expert" if they have an agreement ≥90% (≥ 18 slides with correct diagnosis), as a "referent" with an agreement between 80% and <90%, "competent" if they are between 70 and <80% and "in training" if they have <70%. Results. Microscopists with expertise (68.6%) had more agreement than those without expertise (48.2%). The competency assessment was acceptable (competent, referent, or experts levels) in 11.8% of the microscopists without expertise and in 52.6% from those with expertise. The agreement was lower using blood smear slides with P. falciparum with low parasitaemia, with P. malariae and with mixed infections. Conclusions. Is the first assessment, we found only one of three microscopists from the Peruvian Amazon is competent fro malaria diagnosis according to the WHO standards. From this baseline data, we have to continue working in order to improve the competency assessment of the microscopists within the frame of a quality assurance system.