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Antemortem diagnosis of rabies is highly desirable in animals for limiting the exposure of this fatal zoonotic viral disease. Molecular approaches offer a sensitive tool for detection of rabies viral genome. However, the sensitivity of antemortem detection of rabies from skin of buffalo by molecular approaches has not been compared so far. Comparison of TaqMan real time PCR and heminested reverse transcriptase PCR (HnRTPCR) was, therefore, undertaken to diagnose rabies from skin biopsy samples collected from eleven clinically rabies suspected buffaloes presented to veterinary clinics, GADVASU, Ludhiana, from different districts of Punjab (India). RNA was extracted from all skin samples and converted to cDNA followed by PCR amplification using both molecular methods. Out of 11 cases incorporated in the study 8 skin samples were diagnosed positive using TaqMan real time PCR and HnRTPCR. FAT on brain tissue procured postmortem established same 8 cases as true positive for rabies. Thus, TaqMan real time PCR well as HnRT-PCR detected rabies with 100% sensitivity, specificity and accuracy. The agreement between the results obtained by these methods was 100%, thereby TaqMan real time PCR and HnRT-PCR are equally effective molecular approaches for antemortem diagnosis of rabies from skin biopsies of buffaloes.