An abattoir survey to determine the prevalence of zoonotic diseases encountered at postmortem examination of organs and carcasses was conducted in Maiduguri municipality, Nigeria, between 2000 and 2009. A total of 1,378,066 animals were examined and slaughtered from which 403,560 were cattle, 381,601 goats, 373,567 sheep and 219,308 camels. Out of these numbers, a total of 14,944 bacterial and parasitic zoonotic diseases were diagnosed which included tuberculosis (67.6%), dermatophilosis (15.8%), mange (16.7%), fascioliasis (1.5%) and hydatidosis (4.3%). Occurrence of the diseases based on sex, species of animals and season of the year did not show any significant difference (P>0.05). It was not possible to get the exact records on breed and age for each slaughtered animal due to poor recording systems at the abattoir. With regards to the type of animals brought for slaughter, almost all animals come from the traditional sector and it was difficult to precisely trace back the geographical origins of all animals slaughtered due to lack of reliable animal identification method and so relating the finding of the study to a particular locality becomes difficult. Species-specific prevalence of tuberculosis was 1.6%, 0.4%, 0.3%, 0.3% for cattle, sheep, goats and camels respectively with a 0.7% crude prevalence. Analysis of the tuberculosis cases showed a high rate of occurrence in cattle (P<0.05) and the most affected organs were the lungs (55.1%) and associated lymph nodes (27.7%) (P<0.05). It was concluded that zoonotic diseases such as tuberculosis, dermatophilosis and mange are endemic in the study area. Abattoir records are invaluable in epidemiological surveillance and other aspects of disease control and
prevention strategies.