The aim of this study was to assess the prevalence pattern of mixed-Plasmodium falciparum malaria infections in Brazil by molecular diagnosis and to address its clinically important features. DNA was extracted from 115 thick blood film P. falciparum human blood positive samples using the phenol-chloroform method, followed by a semi-nested PCR protocol with species-specific primers. Seventy-three percent of P. falciparum single infections and 26.95% of mixed infections were found. Amongst mixed infections, the majority was double infection (96.77%). Our results suggest that the prevalence of one species over the other can be important on weakening P. falciparum malaria clinical symptoms. We confirm that P. falciparum co-infections frequently occur in Brazilian malaria endemic areas, with underestimated diagnosis. The results point to the need of improving microscopy or changing for another accurate diagnosis technique to differentiate among human malaria species, as this is essential to choose the best treatment and control measure for malaria. More investigations are necessary in order to clarify the role of mixed-infections in the severity of P. falciparum disease.