The accuracy, reliability, speed and cost of the methods used for malaria diagnosis are key to the diseases’ treatment and eventual eradication. However, improvement in any one of these requirements can lead to deterioration of the rest due to their interdependence. We propose an optical method that provides fast detection of malaria-infected red blood cells (RBCs) at a lower cost. The method is based on the combination of deconvolution, topography and three-dimensional (3D) refractive index reconstruction of the malaria-infected RBCs by use of the transport of intensity equation. Using our method, healthy RBCs were identified by their biconcave shape, quasi-uniform spatial distribution of their refractive indices and quasi-uniform concentration of hemoglobin. The values of these optical and biochemical parameters were found to be in agreement with the values reported in the literature. Results for the malaria-infected RBCs were significantly different from those of the healthy RBCs. The topography of the cells and their optical and biochemical parameters enabled identification of their stages of infection. This work introduces a significant method of analyzing malaria-infected RBCs at a lower cost and without the use of fluorescent labels for the parasites.