Parasitic infections are a major setback to livestock production in Ghana but the disease situation in many localities is poorly understood. A study to determine the prevalence and distribution of Taenia hydatigena in goats and sheep was carried out in two major municipal abattoirs in Tamale and Wa. A total of 538 goats and 256 sheep were screened for cysts during a cross-sectional survey which revealed a prevalence of 22.34% and 33.96% in goats from Tamale and Wa, respectively, and 22.66% in sheep from Tamale. Infection was common in male and female, young and old animals alike. Animals considered in the study originated from various localities within Northern and Upper West Regions and T. hydatigena infection was thought to be autochthonous, depicting a wide distribution of the cestode infection in small ruminants. Our data represent the importance of T. hydatigena infection in goat and sheep production and provide a base for subsequent epidemiological studies in Ghana.