Investigating the rate of patients with MTHFR C677T and MTHFR A1298C polymorphisms in children with autism spectrum disorder and evaluating the role of Next-generation sequencing NGS in diagnosing causes of autism spectrum disorder. Subjects and method: A cross-sectional descriptive study was conducted on 50 children diagnosed with autism spectrum disorder according to DSM – IV at the Department of Medical Biology and Genetics from September 2019 to September 2020. Results: The rates of genotype MTHFR 677 CC/CT/TT in children with autism spectrum disorder were 70%/26%/4%, respectively. The rates of genotype MTHFR 1298 AA/AC/CC in children with autism spectrum disorder were 28%/60%/12%, respectively. There were 15 different variants in the genes associated with autism spectrum disorder detected by NGS. Conclusion: The rates of genotype MTHFR 677 CC/CT/TT in children with autism spectrum disorder were 70%/26%/4%, respectively. The rates of genotype MTHFR 1298 AA/AC/CC in children with autism spectrum disorder were 28%/60%/12%, respectively. NGS is a useful technique for diagnosing genetic causes of autism spectrum disorder, especially rare variants.