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Microscopy as “field based test” was compared with IS900 blood PCR for the diagnosis and estimationof prevalence of Mycobacterium avium subspecies paratuberculosis (MAP) in domestic livestock withclinical Johne’s disease (JD). Of 252 animals screened, 39.3 and 13.1% were positive by faecal microscopyand blood PCR, respectively. Proportional agreement between “microscopy” and blood PCR was substantial.1262 faecal samples from animals suspected of clinical JD were screened by microscopy in 2009-2010 and41.3% were positive. Prevalence of MAP was highest in cattle (61.8%), followed by goats (41.3%), sheep(33.4%) and buffaloes (15.7%). Faecal microscopy was cost effective, easy to adopt and repeatable for thescreening of domestic ruminant population against MAP infection.