A 2-year-old boy presented for the evaluation of left nonpalpable testis. Laparoscopic examination revealed right migratory testis without any abnormal appearance and a uterine-like structure with an immature gonad in rectovesical fossa. Right spermatic duct merged into the uterine-like structure on the right side. The immature gonad was removed by laparoscopic procedure, while the uterine-like structure was not removed to preserve the right spermatic duct. Right orchidopexy was also performed. Histopathologic diagnosis for the removed gonad was hypoplastic testis. After the chromosomal analysis, 46 XY karyotype, we diagnosed this case as persistent Müllerian duct syndrome. Persistent Müllerian duct syndrome diagnosed by laparoscopic examination is very rare. To the best of our knowledge, this is the third case in Japan.