Background: Congenital anomalies involve changes that may occur in the central nervous system during the period from gestation until birth. The present study reports a case of cranioschisis and anencephaly in a dog and aims to discuss the possible etiologies of these malformations in dogs.Case: A pinscher bitch was referred to a private veterinary clinic in the city of Muriaé - MG, for routine consultation and gestational diagnosis, which was carried out by ultrasound on the 39th day. Routine care was extended until delivery, and clinical and complementary examinations were performed to assess the health of the female dog and that of the fetuses. Vital parameters and morphological characteristics showed that all fetuses had present cardiac activity, correctly formed bone skeleton, definition of the head, trunk and limbs, presence of fetal movements, definition of the hepatic region and hepatic parenchyma typically hypoechoic, hyperechoic pulmonary parenchyma, and visualization of the stomach and bladder. The delivery lasted two hours, and three female puppies were born. A macroscopically significant cranial alteration was observed in the second pup; it was located in the middle line of the skull unprotected by skin. The placenta was dark in color. The puppy’s respiratory activity was present, but with dyspnea, body movements were limited and presented hypothermia. In the first 24 h, the female puppy was fed homemade milk compound through a syringe because of difficulty in performing the suction movement. Delay in urination and defecation were also observed in relation to the other neonates. Before completing the first 48 hours of birth, this newborn died, and his cadaver was submitted for necropsy. The necropsy procedure identified the presence of acrania (partial absence of the bones of the skull), aplasia of the skin of the eyes, meningoencephalocele demonstrating that the meningeal formed an external pocket, and partial anencephaly and exencephaly (brain outside the cranial cavity). Subsequently, organ samples were sent for evaluation by means of qualitative PCR for canine herpesvirus and the result was negative.Discussion: Anencephaly is a result of erroneous closure of the neural sulcus, causing partial formation or no formation of the brain. The etiology ranges from environmental factors or teratogenic effects such as radiation, viruses, toxic substances, maternal diseases, maternal genotype, enzymatic activity, and fetal susceptibility. CaHV-1 type 1 canine herpesvirus has been reported to cause abortion, fetal mummification, stillbirth, the birth of weak pups, or neonatal death. The anomalies involving cranial and encephalic malformation have a multifactorial etiology, which made it difficult to identify the actual cause that led the pup to present the reported characteristics. Despite the negative result of the PCR test, Canine herpesvirus (CaHV-1 type 1), as well as the use of some drugs during pregnancy, are major causes of this disease.