Autism spectrum disorder (ASD) is a neurodevelopmental disorder with onset in early childhood. While highly heterogeneous, the core manifestations always include persistent difficulties in social interaction and communication, as well as a pattern of restricted interests, repetitive behaviours, and abnormal sensory processing [1]. In addition, psychiatric comorbidity is high [2], and there are genetic risk overlaps with some other mental and neurodevelopmental disorders. In the vast majority of cases, the condition persists into adulthood [3], albeit with various behavioural features and variable mental and somatic comorbidity over a given lifespan. ASD is associated with high societal, educational, and health care costs, and, in many cases, a dramatic impact on the quality of life of patients and their families. ASDs are highly heritable [4], and a multitude of genetic studies have been published. In addition, more recent reviews also emphasize the role of genetic and environmental factors in the pathophysiology of ASD [5,6], which are mediated by lasting epigenetic changes. The genetic architecture of ASD comprises common and rare variations as well as cytogenetic disturbances, such as copy number variations, translocations, inversions, and numerical chromosomal aberrations [7]. Based on the genes affected and the respective functional effects, the idea of personalised medicine is to eventually use that information for the development of targeted treatments or towards the ability to predict the response to a specific intervention, mainly pharmacological but also psychosocial, given the individual's genetic and environmental risk constellation. The current Special Issue aims to highlight some core aspects regarding basic and applied science approaches in advancing this field of science. Currently, psychopharmacological treatment in ASD can improve many comorbid neurodevelopmental disorders, such as attention-deficit/hyperactivity disorder or aggressive behaviour, and the core symptoms of restricted and repetitive behaviours [8,9]. No pharmacological options targeting social interaction and communication are available. Social communication and other strongly relevant targets of intervention in ASD [10], such as adaptive behaviour, cognitive and language development, or quality of life may be improved by early behavioural intervention [11]. Still, individual outcomes are highly variable, even with the same kind of psychosocial intervention approach. A better understanding of the pathophysiological mechanisms underlying this broad range of symptoms and abilities, as well as their longitudinal course, is a crucial first step towards the development of personalised treatments. Given the heterogeneity regarding the ASD phenotype and its underlying etiology, such as diverse genetic variation and additional environmental risks with the related neurobiological mechanisms, discovering new pharmacological treatments for the condition is a huge challenge. This challenge is at the heart of this Special Issue. Here, we have collected a set of contributions providing state-of-the-art coverage, ranging from the theoretical framework, linking genetics to human behaviour and therapy, to initial practical examples of how genetics can provide valuable insights into the personalized clinical management of autistic individuals. To introduce the papers of this Special Issue, a broad summary of the many challenges related to the development of personalised medicine in ASD is given here. In the final statement from the editors, the specific contributions of the articles included in this Special Issue will be summarised.