Rationale: Congenital absence of either a part of or the entire sacrum is rare, and only a few such cases have been reported until now. Most cases showed vertebral, pelvic, neurological, and visceral abnormalities, and the cases were usually quite serious. Only in rare cases was there urine retention without other symptoms. Patient concerns: We describe the case of a 28-years-old man who presented with urine retention. Diagnoses: Urodynamic study confirmed that he had urinary retention, and magnetic resonance imaging (MRI) showed the absence of the sacrum. Interventions: He was treated with electro-acupuncture and medications to improve nerve function. Outcomes: His symptoms showed clear improvement. Lessons: Although this case is rare, it indicates that the spine and pelvis may need to be examined when unexplained urinary retention occurs.