To investigate the association of spinal anomalies with lumbar spondylolysis and spina bifida occulta (SBO). A total of 1190 patients with thoracic, abdominal, and pelvic computed tomography scans available were categorized according to the number of presacral (thoracic and lumbar) mobile vertebrae and the presence or absence of lumbosacral transitional vertebrae (LSTV). The prevalence of spondylolysis and SBO and the association of spinal anomalies with these disorders were evaluated. Normal morphology (17 mobile vertebra with no LSTV) was found in 607 men (86.5%) and 419 women (85.9%) and about 14% of patients had anomalies. Spondylolysis was found in 74 patients (6.2%), comprising 54 men (7.7%) and 20 women (4.1%). SBO involving the lumbar spine was found in 9 men (1.3%) and 2 women (0.4%). Spondylolysis was significantly more common in men with 18 vertebrae without LSTV (21.1%) than in those with 17 vertebrae without LSTV (7.2%) (p = 0.002). The prevalence of spinal anomalies was 55.6% in men and 50.0% in women with SBO that included a lumbar level was significantly higher than in both men (13.5%, p < 0.001) and women (4.8%, p = 0.003) without SBO. These findings indicate that there is a relationship between spinal anomalies and both spondylolysis and SBO, which may lead to elucidation of the mechanism of onset of spondylolysis and improve its treatment and prognosis. Awareness that patients with SBO involving the lumbar spine have an increased likelihood of a spinal anomaly may help to prevent level errors during spinal surgery.