The main objective of this pilot project was to determine the co-transmission of Malaria, Dengue, Zika and Chikungunya in the Peruvian Amazon (Iquitos) and North coast (Piura) using a differential diagnosis by molecular methods. The analytic cross-sectional study was carried out during the summer of 2018 in communities with high co-transmission of Malaria and Dengue based on records from the Ministry of Health.