The present study aimed to provide evidence for the genetic heterogeneity of familial autism spectrum disorder (ASD), which might help to improve our understanding of the complex polygenic basis of this disease. Whole-exome sequencing (WES) was performed on two autistic children in a family pedigree, and reasonable conditions were set for preliminarily screening variant annotations. Sanger sequencing was used to verify the preliminarily screened variants and to determine the possible sources. In addition, autism-related genes were screened according to autism databases, and their variants were compared between two autistic children. The results showed that there were 21 genes respectively for autistic children IV2 and IV4, preliminarily screened from all variants based on the harmfulness (high) and quality (high or medium) of the variants, as well as the association between mutant genes and autism in human gene mutation database. Furthermore, candidate autism-related genes were screened according to the evidence score of >4 in the Autism KnowledgeBase (AutismKB) database or >= 3 in the AutDB database. A total of 11 and 10 candidate autism-related genes were identified in the autistic children IV2 and IV4, respectively. Candidate genes with an evidence score of >16 in AutismKB were credible autism-related genes, which included LAMC3, JMJD1C and CACNA1H in child IV2, as well as SCN1A, SETD5, CHD7 and KCNMA1 in child IV4. Other than the c.G1499A mutation of SCN1A, which is known to be associated with Dravet syndrome, the specific missense variant loci of other six highly credible putative autism-related genes were reported for the first time, to the best of the authors' knowledge, in the present study. These credible autism-related variants were inherited not only from immediate family members but also from extended family members. In summary, the present study established a reasonable and feasible method for screening credible autism-related genes from WES results, which by be worth extending into clinical practice. The different credible autism-related genes between the two autistic children indicated a complex polygenic architecture of ASD, which may assist in the early diagnosis of this disease.