Purpose: The aim of this article was to compare longitudinal changes in hip morphology in cerebral palsy (hypertonic) and spinal muscular atrophy (hypotonic) to examine the influence of muscle tone on development of hip displacement. Methods: Children with spinal muscular atrophy (Types I and II) and cerebral palsy (Gross Motor Function Classification System IV and V) with hip displacement (migration percentage >30%) were included. Head shaft angle, migration percentage, and acetabular index were measured at T1 (1–2.5 years), T2 (3–5 years), and T3 (6–8 years). Analysis of variance testing and linear regression were utilized. Results: Sixty patients (cerebral palsy, N = 41; spinal muscular atrophy, N = 19) were included. Hip displacement occurred earlier in spinal muscular atrophy (34 months) than cerebral palsy (49 months) (p = 0.003). Head shaft angle was high and did not change between T1, T2, and T3, but significant changes in migration percentage were found (cerebral palsy: 23%, 36%, 45% (p < 0.01) and spinal muscular atrophy: 37%, 57%, 61% (p = 0.02)). Migration percentage increased by age in cerebral palsy (r = 0.41, p < 0.001), but not in spinal muscular atrophy (r = 0.18, p = 0.09). Acetabular index increased with migration percentage (cerebral palsy: r = 0.41, p < 0.001; spinal muscular atrophy: r = 0.48, p < 0.001). Conclusion: Persistent lateral physeal tilt by head shaft angle was found for both spinal muscular atrophy and cerebral palsy. Abnormal physeal alignment may be causally related to weakness of the hip abductor muscles rather than spasticity or muscle imbalance, resulting in coxa valga and secondary acetabular dysplasia. Level of evidence: III (case–control study).