BackgroundPrevalence of placental malaria has been widely used as a standard indicator to characterize malaria infection in epidemiologic surveys. Placental malaria poses a greater diagnostic challenge, accurate and sensitive diagnostic tool for malaria infections in pregnancy is needed.MethodsA cross sectional study was conducted at Medani Hospital, which serves catchment area which is characterized by unstable malaria transmission. One hundred and seven placentae were investigated for malaria infection using polymerase chain reaction (PCR) and histology.Resultsout of 107 investigated placentae, 33 (30.8%) and 34 (31.8%) were positive for malaria by histology (two (2%) and 31(29.0%) were acute and past infections, respectively) and PCR, respectively. Out of 33 positive by histology, 15 were positive by the PCR while 18 were negative. The sensitivity of the PCR was 45.5% (95% CI: 29.2%- 62.5%). Out of 74 which were negative by histology, 19 were positive by the PCR. This is translated in specificity of 74.3% (95% CI: 63.5%- 83.3%). Of those tested positive by the PCR, 15 were positive by the histology, while 19 were negative. This is translated into a positive predictive value of 44.1% (95% CI: 28.3%- 61.0%). Of those 73 tested negative by the PCR, 55 were negative according to histology while 23 were positive. This is translated into a negative predictive value of 75.3% (95% CI: 64.5%-84.2%).ConclusionPCR had low sensitivity and specificity in comparison to placental histology, perhaps because the vast majority of the placental infections were past infections. Further research is needed.