BACKGROUND: In order to better understand the underlying biological mechanism/s involved in autism, it is important to investigate the cognitive and behavioural phenotypes associated with idiopathic autism (autism without a known cause) and comorbid autism (autism associated with known genetic/biological disorders such as fragile X syndrome). Parental effects associated with each type of autism also serve to cast light on the biological underpinnings of autism. METHOD: Forty-nine participants with idiopathic autism (AD; Mean age: 11.16; SD: 6.08) and their parents (45 mothers; 34 fathers), and 48 participants with fragile X syndrome and co-morbid autism (FXS/AD; Mean age: 17.30; SD: 10.22) and their parents (32 mothers; 30 fathers) were administered the ADOS-G and the age-appropriate Wechsler test to ascertain autism and cognitive profiles respectively. RESULTS: The AD and FXS/AD groups showed a similar profile on the ADOS domains, with slightly higher scores on the Communication domain in the FXS/AD group, after adjusting for full-scale IQ. Marked differences between the groups in their cognitive abilities were apparent, with the FXS/AD group showing significantly lower scores on all subtests except Comprehension. While no parental effects were found for the FXS/AD group, a paternal effect was apparent on the combined ADOS score for the AD group. Moreover, midparental effects were found in this group for full-scale IQ (FSIQ) and verbal IQ (VIQ). Analyses also revealed parental effects for the subtests of Similarities, Vocabulary, and Information with predominantly maternal effect, and Digit Span with predominantly paternal effect. Both parents contributed to the midparental effect for Processing Speed. CONCLUSIONS: The results, together with our previous findings, suggest that the postulated combination of susceptibility genes for autism may primarily involve cognitive rather than behavioural processes.