Congenital malformations affecting the lower respiratory tract of non-human primates are extremely rare, with only a few published reports. We report a complex case of multiple congenital lung malformations in a 1-year-old female black-capped Bolivian squirrel monkey (Saimiri boliviensis boliviensis) that died following an anaesthetic procedure for tattoo placement. At necropsy, the left lung lobes had severe pulmonary hypoplasia. The left medial lung lobe had a long stalk that ended with multiple air-filled cysts and bullae, characteristic of congenital lobar emphysema. Histologically, at the margin of the left cranial lung lobe was a 2 mm diameter mass composed of multiple cystic structures lined by a cuboidal epithelium and supported by thick trabeculae of myxoid stroma and dense connective tissue containing capillaries. The histological morphology of the mass was consistent with congenital pulmonary airway malformation type 4, an exceedingly rare condition in both human and veterinary medicine.