OBJECTIVES: Autism, a heterogeneous disease, is described as a genetic psychiatry disorder. Multiple lines of evidence support the notion that most cases of autism likely have an underlying genetic cause or predisposition. Since folate and   methylation   (single   carbon   metabolism)   are   vital   in neurological development, we routinely screened children for the common  mutations  of  the  methylenetetrahydrofolate  reductase gene  (MTHFR),  which  regulates  this  pathway. Common   polymorphisms   in   the   MTHFR gene   have   been associated  with  reduced  enzyme  activity.. The study aims to analyze the chromosome alterations and rare mutations in MTHFR and its association in Autism patients. METHODS: In the present study, in order to investigate the possible cytogenetic damage using peripheral blood lymphocyte culture (PBLC), and rare mutations of MTHFRthat have been reported to be associated with autism patients using PCR – SSCP method, and was carried out in the 25 autistic patient samples, based on the detailed DSM - IV questionnaire, and equal number of controls were selected. RESULTS: In our study chromosomal alterations were frequently observed in chromosomes 2, 3, 7, 22 and X (2q32, 3q25-q27). In the present study, chromosomal aberrations showed higher degree in experimentals compared to controls (P<0.001). We analysed the association between three single nucleotide polymorphisms (SNPs) of the MTHFR gene. No significant evidence between any SNPs of MTHFRgene in autism was observed. CONCLUSIONS: In conclusion, in this pilot study, we observed that the identification of cytogenetic abnormalities is not only important for providing a cause for the autism in a single individual but is also critical for accurate counselling regarding recurrence risks to parents and family members. We suggest that MTHFRmight represent a major susceptibility gene for autism.