The lymphoepithelial cyst (LEC) of the major salivary gland is a rare lesion described in medical literature. It is found in human immunodeficiency virus (HIV)-infected patients and considered an early manifestation of this infection. Despite the variety of theories, the origin of this lesion remains controversial. No veterinary studies on LEC have been published so far. This study is the first-ever that aims to describe histopathological, histochemical, and immunohistochemical features of a LEC located adjacent to the salivary gland of a goat. The goat proved seropositive for the small ruminant lentivirus, showed clinical signs of caprine arthritis-encephalitis, and had caprine arthritis-encephalitis virus (CAEV)-infected cells in the lung. The histopathology revealed a cystic lesion lined mainly with squamous epithelium surrounded by a lymphoid component, containing a mucus-negative material and a few nonbirefringent structures corresponding to amylase crystalloids. Using immunohistochemistry, CAEV-positive cells were detected in macrophages, LEC epithelial cells, and the salivary gland. The B cells were mainly in the germinal centres, the intraepithelial lymphocytes expressed CD3 and Bcl-2, and the proliferative activity was low. This study showed that LEC had many similar histological and immunohistochemical features to those seen in humans. However, further studies are required in this respect.