Purpose To investigate the spinopelvic alignment and vertebral shape in children, and associations with body composition and structural spinal abnormalities on magnetic resonance imaging (MRI). Methods We performed a cross-sectional study embedded in the Generation R Study, a prospective population-based birth cohort. Pelvic incidence and vertebral concavity ratios for each lumbar level were determined on sagittal MRI images in 9-year-old children, and structural spinal abnormalities were scored semi-quantitatively. The BMI-SD score was calculated, and body composition was assessed using DXA scans. Associations of pelvic incidence and vertebral concavity ratios with structural abnormalities and body composition measures were assessed using (multilevel) regression analyses. Results This study included 522 participants (47.7% boys), aged 9.9 years (IQR 9.7–10.0). The mean pelvic incidence was 36.6° (SD 8.0). Vertebral concavity ratios ranged from 0.87 to 0.90, with significantly lower ratios for boys compared to girls. Associations were found for a larger pelvic incidence with decreased disc height [OR 1.03 (95% CI 1.02–1.05)], and a pelvic incidence in the lowest tertile with less disc bulging [OR 0.73 (95% CI 0.56–0.95)]. Increased vertebral concavity ratio was associated with decreased disc height [OR 14.16 (95% CI 1.28–157.13)]. Finally, increased fat-free mass index was associated with a smaller pelvic incidence [adjusted OR 0.85 (95% CI 0.07–1.63)]. Conclusion The mean pelvic incidence of 9-year-old children is 36.6° on supine MRI images, and a slightly concave shape of the lumbar vertebrae is seen. Spinopelvic alignment is associated with structural spinal abnormalities, and might itself be influenced by the children’s body composition.