Several neurodevelopmental disorders are associated with a higher prevalence of atypical laterality (e.g., left-handedness). Both genetic and non-genetic factors play a role in this association, yet the underlying neurobiological mechanisms are largely unclear. Recent studies have found that stress, mediated by the hypothalamic-pituitary-adrenal (HPA) axis, could be linked to laterality development. These findings provide an opportunity to explore new theoretical perspectives on the association between atypical laterality and neurodevelopmental disorders. This article aims to provide a theoretical framework demonstrating how perinatal adversities could disrupt the typical developmental trajectories of both laterality and neurodevelopment, potentially impacting both the HPA axis and the vestibular system. Additionally, we argue that the relationship between atypical laterality and neurodevelopmental disorders cannot be understood by simply linking genetic and non-genetic factors to a diagnosis, but the developmental trajectories must be considered. Based on these ideas, several perspectives for future research are proposed.