Epididymal agenesis is described as the complete or partial lack of the epididymis. In this paper, a two-year-old Pekingese dog with epididymal agenesis is reported during routine castration. The dog was presented to a private pet hospital for conventional castration. Anatomically unilateral epididymal agenesis was observed during orchiectomy. Also, pathologically segmental unilateral epididymal agenesis and atrophy of testis were implied. The dog was neutered. Epididymal agenesis is a highly rare phenomenon in all breeding dogs. To the authors’ knowledge, this is the first report of epididymal agenesis in small breeding dogs. This kind of animal should not use for breeding programs and practitioners pay attention to this anomaly while encountered infertility in dogs.