The purpose of this study was to assess the risk of neuro-orthopaedic malformations after in-vitro fertilization. We compared the prevalence of neuro-orthopaedic malformations in two groups of pregnancies conceived either naturally or by in-vitro fertilization, and used multivariate analysis to study the impact of each variable. The results showed a prevalence of 0.89% neuro-orthopaedic malformations in the in-vitro fertilization cohort and 0.32% in the natural conception cohort. The three times greater risk of malformations in the in-vitro fertilization cohort was reduced after adjustment to other variables. We concluded that the increased risk of neuro-orthopaedic malformations after in-vitro fertilization is not due to the technique itself but rather to factors associated with it.