Objective. To determine the cost-effectiveness ratios of three options for diagnosing malaria at the local health provider in 50 communities near the Peruvian Amazon. Methods. Calculation of the incremental cost-effectiveness ratios of three options for diagnosing malaria-not using rapid tests, using rapid tests, and accessing microscopy-in patients presenting with fever in 50 communities near Iquitos in the Peruvian Amazon, communities with limited access to microscopy that depend on a network of local health providers. The incremental costs and effects of the two latter options were calculated and compared with the first option (currently in use). By dividing the incremental costs among the incremental effects, the incremental cost-effectiveness ratio was calculated. Results. Using rapid tests would save the Ministry of Health of Peru: US$ 191 for each new case of Plasmodium falciparum malaria treated promptly and appropriately; US$ 31 per new case of P. vivax malaria treated promptly and appropriately; US$ 1 051 per case of acute malaria averted; and US$ 17 655 for each death avoided. Access to microscopy by all the communities would generate an additional cost of: US$ 198 per new case of P. falciparum malaria treated promptly and appropriately; US$ 31 per new case of P. vivax malaria treated promptly and appropriately; US$ 1 086 per case of acute malaria averted; and US$ 18 255 for each death avoided. Conclusions. The use of rapid tests by local health providers can improve the effectiveness of malaria diagnosis in patients with fever in the 50 communities studied, at a cost lower than the current method. The recommendation is to expand the use of rapid tests among the health providers in communities similar to those studied.