Intronic single nucleotide polymorphisms (SNPs) in the clock genes _npas2_ and _per1_ and the homeobox gene _en2_ are reported to be associated with autism. This bioinformatics analysis of the intronic regions which contain the autism-associated SNPs rs1861972 and rs1861973 in _en2_, rs1811399 in _npas2_, and rs885747 in _per1_, shows that these regions encode RNA transcripts with predicted structural characteristics of microRNAs. These microRNA-like structures are disrupted _in silico_ by the presence of the autism enriched alleles of rs1861972, rs1861973, rs1811399 and rs885747 specifically, as compared with the minor alleles of these SNPs. The predicted gene targets of these microRNA-like structures include genes reported to be implicated in autism (_gabrb3_, _shank3_) and genes causative of diseases co-morbid with autism (_mecp2_ and _rai1_). The inheritance of the AC haplotype of rs1861972 - rs1861973 in _en2_, the C allele of rs1811399 in _npas2_, and the C allele of rs1234747 in _per1_ may contribute to the causes of autism by affecting microRNA genes that are co-expressed along with the homeobox gene _en2_ and the circadian genes _npas2_ and _per1_
