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Coenurus gaigeri is the larval stage of Taenia multiceps gaigeri, which infects the muscles of goats and, to a lesser extent, sheep. Metacestodes of the goat such as Coenurus cerebralis, Cysticercus tenuiollis, Cysticercus ovis, and hydatid cysts have been extensively studied. However, because of the uncommon occurrence of C. gaigeri, very few records exist of its biology, pathogenesis, and pathology. Therefore, an investigation was conducted in the summer of 2008 at Shiraz Slaughterhouse, where 2.6% of the goats were infected with intramuscular cysts. Scolices from coenuri were collected for morphologic analysis, and the cysts were identified as C. gaigeri, the intermediate stage of T. multiceps gaigeri. In addition, molecular genetic markers of mitochondrial DNA were applied phylogenetically to resolve the questionable relationship between C. gaigeri and C. cerebralis. All coenuri fluids were aspirated and centrifuged separately; the supernatants were analyzed for biochemical features that included glucose, total protein, urea nitrogen, uric acid, triglycerides, cholesterol, creatinine, calcium, sodium, potassium, alanine aminotransferase, and aspartate aminotransferase. The pathologic changes around the coenuri included mechanical destruction of the affected tissues, associated with degenerative and necrotic changes, infiltration by polymorphonuclear and mononuclear cells, proliferation of fibroblasts, and development of adventitious tissue. Results based on phylogenetic analysis of the mitochondrial DNA (CO1 and ND1) suggest that the larval stages of T. multiceps gaigeri and C. cerebralis, which showed similar morphological criteria, are monophyletic species. However, C. gaigeri interestingly were situated in the biceps femoris, triceps, and abdominal muscles without localization in the nervous system.