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Abstract Background Anorectal malformations (ARM) represent a wide spectrum of defects. Caudal and genitourinary malformations can associate with anorectal malformations. Genetic factors may play role in the development of anorectal malformations. Perineal masses like sacrococcygeal teratoma, rectal prolapse, or duplication cysts were reported before, but their association with perineal hamartoma and anal atresia is extremely rare. Case presentation Here, we report an 11-month-old female infant. She had 551 kb duplication at 7p12.3 with perineal hamartoma and anal atresia consisting a cystic lesion with a diameter of 4 mm at the filum terminale (L2 vertebra) on lumbar magnetic resonance imaging (MRI) in neonatal period. She presented with hypotonia. She had anorectal anomaly and external perineal mass bulging from left major labium extending across anal region with imperforate anus. There was 1 × 1 cm polyp-like protrusion on it. She was operated in neonatal period. Genetic laboratory investigations showed karyotype 46, XX. The microduplication of the chromosome 7p12.3 was detected by microarray analysis. There were not any significant homozygous or heterozygous variants determined by whole-exome sequencing. Conclusions To the best of our knowledge, this is the first report of a patient with a microduplication of the chromosome 7p12.3, and second case with perineal hamartoma and imperforate anus. Clinicians should pay attention to microdeletions and microduplications while giving genetic counseling to patients with urogenital and anorectal abnormalities.