This study was conducted to investigate the prevalence of besnoitiosis and associated histopathological changes amongst apparently healthy cattle and goats at slaughter in Maiduguri central abattoir Borno state, Nigeria. A total of 100 skin sections each, from the neck region were randomly collected, preserved in 10% formalin and later taken to the laboratory and subjected to histopathology to detect Besnoitia cysts and associated histopathological changes. This study revealed an overall prevalence of 2% in cattle. Out of the 100 skin sectionsexamined from cattle, 38 were from bulls and 62 were from cows. Of the 38 skin sections from bulls examined, 2 (5.3%) were positive for Besnoitia cyst and none (0%) was positive for the cow’s (P> 0.05). Similarly, of the 100 skin sections examined, 80 were from Wadara breed and 20 from Red bororo. Out of the 80 skin sections examined from Wadara breed, 2 (2.5%) were positive for Besnoitia cyst and none (0%) was positive for Red bororo (P> 0.05). However, out of 100 skin sections from goats examined, none was positive for Besnoitia cysts revealing 0% prevalence. All the skin sections sampled and examined were from adult cattle and goats. Out of the 100 skin sections examined from the adult cattle, 2 (2.0%) were positive for Besnoitia cysts. A skin section examined from Wadara breed showed localized area of suppurative dermatitis in the dermis of the skin characterized by massive neutrophilic infiltrations. This is the first report showing the prevalence of besnoitiosis in apparently healthy cattle and goats in Borno state, north eastern Nigeria.