A Taqman assay for the detection of pathogenic Leptospira was modified to suit the LightCycler instrument. The modified assay was found to have an analytical sensitivity of 10 copies/reaction. The assay was then compared to the current gold standard for acute phase detection, culture, and to a commercially available Leptospira-specific IgM enzyme-linked immunosorbent assay (ELISA). Of the 236 samples including serum and ethylenediaminetetraacetic acid anticoagulated blood sample submitted for testing, polymerase chain reaction (PCR) was able to detect Leptospira DNA in 27 of the 28 culture positives and in 1 negative culture. Discrepant results were resolved by using the microscopic agglutination test on convalescent sera. The PCR was found to have a clinical specificity and sensitivity of 99.5% and 96.4%, respectively, when compared to the culture. Comparisons between culture and ELISA showed that the ELISA lack sensitivity (4.2%) and positive predictability (3.6%) for the detection of acute phase Leptospira infections. These results show that the modified LightCycler Taqman assay could be used as a replacement of culture for the detection of pathogenic Leptospira in a clinical setting.