The infection rates of domestic large and small ruminants with M. paratuberculosis were studied at slaughter house. From each animal, smears were taken from terminal ileum (TI), ileocecal valve (IV), ileocecal lymph node (ILN), rectum mucous membrane (RMM), and feces (F). They were stained by Ziehl Neelsen staining method. During this study, 218 cattle, 48 buffaloes, 379 sheep, and 42 goats were examined. The infection rates were 1.48%, 6.25%, 1.8%, and 4.76% for the above mentioned species, respectively. The comparative identification rates of infected animals by each of TI, IV, ILN, RMM, and F samples in large and small ruminants were 100% and 100%, 100% and 100%, 85.7% and 100%, 100% and 58.7%, 57.1% and 55.5%, respectively. The infection rates in Holstein and native breeds were 2.86% and Nil respectively and in cattle no infection was diagnosed in the age less than 2 years. In small ruminants, the infection rates in two different localities were 1.9% and 6.25% and in two different age groups were 0.9% and 2.9%.