A 1.5-year-old, entire male mongrel dog with a bifid nose and primary cleft palate showed aggressiveness towards unknown dogs despite having adequate canine socialisation and the absence of previous traumatic experiences; furthermore, he does not exhibit sexual behaviour towards females in heat. He was previously treated for fear-related aggression towards unknown people and environmental phobia due to poor human socialisation. Pharmacological treatment with fluoxetine and trazodone, together with behaviour modification, was started without success. Therefore, it was decided to repeat medical tests. CT and MRI revealed a rostral middle raphe ossification defect incompatible with the presence of the vomeronasal organ (VNO) and the absence of the septum pellucidum (SP). The dog was presumptively diagnosed with aggressiveness towards unknown dogs due to an organic cause, a congenital anomaly with agenesis of the VNO and SP. This case shows the importance of both structures in the regular intraspecific interactions of dogs.