Cystic echinococcosis (CE) is a chronic parasitic disease caused by the larval stage of Echinococcus granulosus. It is considered a major zoonotic concern globally, particularly in regions where livestock such as sheep are raised in close contact with dogs, the definitive hosts of the parasite. In Albania, CE remains endemic, affecting both humans and domestic animals. The current study was conducted in the Korça region in southeastern Albania, to determine the prevalence, distribution, and characteristics of hydatid cysts in sheep slaughtered at local abattoirs. Between January and December 2024, a total of 1,072 sheep were inspected post-mortem. Organs, including the lungs and liver, were examined for the presence of hydatid cysts, and infected tissues underwent both macroscopic and histological evaluation. Hydatid cysts were detected in 19.8% (n = 213) of the animals. Pulmonary involvement was slightly more common (53.5%) than hepatic (46.5%). Among the identified cysts, 71% were fertile, 26.7% sterile, and 2.3% calcified. Histomorphological analysis revealed significant fibrotic and inflammatory changes in affected organs, with more advanced lesions seen in older sheep. The presence of collagen fibers surrounding the cysts was confirmed using Masson’s trichrome staining. These findings provide valuable insight into the epidemiological burden of hydatidosis in southeastern Albania. Understanding the distribution and fertility of cysts is essential for evaluating the risk of transmission and for designing effective control strategies aimed at limiting the spread of this zoonosis among both livestock and human populations.