In order to ascertain and evaluate mothers' perceptions of the sexual development and behavior of their children with autism, we conducted a questionnaire survey on participants in meetings held in Nagasaki. From among 172 persons who consented to participate in the survey and responded to the self-administered questionnaire, we selected 71 mothers of sons with autism (aged 6 years or over) as the study subjects. The questionnaire included items on children's sexual behaviors, the appearance of secondary sexual characters/sexual development, the mothers' perceptions of the children's sexual development and behavior, and assessments of their own child and persons with autism in general with respect to masturbation, romantic relationships, and marriage. According to the severity of the children's autism, subjects were classified into severe and non-severe groups and the above-mentioned items were compared between the two groups. No significant difference was observed between the two groups in terms of the age at first appearance of secondary sex characters; however, the age at which interest in the opposite sex was first shown was significantly earlier in the non-severe group (p = 0.031). Among 58 children aged 120 months or over, 29 (50.0%) were masturbating and the proportion of such children was significantly larger in the severe group (p = 0.014). Regarding problem sexual behavior, no significant difference was observed in the frequency of worried mothers between the two groups (p = 0.80), while “talking about sex in public” was more frequent in the non-severe group (p = 0.018). Approximately 80% of the mothers in both groups had positive views about masturbation both for their own child and for persons with autism in general; however, the proportion of mothers showing positive views about romantic relationships or marriage was significantly smaller in the severe group (p < 0.0001). The present study demonstrated that mothers' perceptions of sexual development and behavior in their children with autism vary according to the disease severity. This finding indicates the necessity for healthcare professionals to actively concern themselves with the mothers.