Autism spectrum disorder (ASD) is a childhood-onset neurodevelopmental disorder characterized by persistent deficits in social communication and social interaction and the presence of restricted, repetitive patterns of behavior, interests, or activities. The heritability of ASD is estimated to be more than 90%. The genetic basis of ASD is heterogeneous and complex and involves multiple genes, gene–gene interactions, and gene–environmental interactions. The genetic landscape of ASD has started to come to light, thanks to recent advances in molecular genetic technology. Conventional karyotyping analysis revealed aberrations in the chromosomal number and structure in 5%–10% of ASD cases, and a recent array-based comparative genomic hybridization assay found that an additional 10%–15% of ASD cases had submicroscopic copy number variations (CNVs) in DNA segments. Ongoing whole genome and exome sequencing studies have also started to reveal more novel genetic variants at the single-nucleotide level associated with ASD. These genomic and genetic variants are usually rare and present in individual families through inheritance or de novo mutations. In addition, genome-wide association studies discovered several common polymorphic variants associated with ASD.We summarize the current findings of these variants in this review article. The list of these variants is far from complete. However, their discovery enables researchers to begin investigating the neurobiology of ASD with the hope of finding new medicines for treating ASD.