Background: Microscopic detection is the conventional method for detecting malaria parasites. Although it is efficient and inexpensive, it has its limitations. In recent years, polymeras chain reaction (PCR) has been considered superior to microscopy in detecting mixed Plasmodium infections or infections with low parasite density. To determine whether microscopic or nested PCR (nPCR) is better at detecting congenital malaria (CM). Methods: Blood smear examination and nPCR were performed with blood samples taken from mothers and their newborns, who were likely to be suffering from CM and in whom one of the symptoms was low birth weight (LBW). The sensitivity and specificity of each method were then compared. Results: During one year of study, the prevalence of CM among 92 LBW newborns was determined to be 6.8% using microscopy and 7.8% using nPCR. Among the 92 mother–infant paired subjects, CM was detected in 34 subjects (37%) by microscopy and in 39 subjects (42.4%) by nPCR. nPCR was more sensitive (76.5% vs 66.7%) but less specific (77.6% vs 84.9%) than microscopy. When the two methods were compared, nPCR gave significantly better results in diagnosing CM (AUC = 0.770; P < 0.001). Conclusion: Although microscopy remains the most appropriate method for the diagnosis of CM in remote areas, nPCR can be considered a complementary test.