Background Different diagnostic techniques have been used in the diagnosis of schistosomiasis. However, they are far from ideal regarding its early diagnosis. PCR techniques have been tried to improve the direct detection of schistosomiasis. Objective The aim of the present study was to evaluate the diagnostic performance of direct amplification of Schistosoma mansoni DNA in the early prepatent period in experimentally infected mice by PCR technique using unextracted DNA as PCR template compared with pre-extracted S. mansoni DNA samples. Materials and methods Mice were infected by 100±10 S. mansoni cercariae. Three mice were sacrificed every 3 or 4 days for 5 weeks. Whole blood samples were collected for direct amplification without prior extraction. Serum samples were pooled, and the extracted DNA was detected by using the KAPA blood PCR kit and conventional PCR methods. The diagnostic performance was compared between the two methods. Results The results showed that the diagnosis of S. mansoni utilizing pre-extracted DNA was superior to direct amplification of DNA, bypassing nucleic acid extraction which failed to detect S. mansoni DNA in any of the examined samples. Pre-extracted DNA was detected in all samples from the second day after infection by using the two PCR techniques. Conclusion These results indicate that S. mansoni infection cannot be efficiently detected directly by using the PCR technique without pre-extraction of DNA from whole blood samples using the KAPA blood PCR kit.