Language-impaired individuals with autism perform poorly on tests such as non-word repetition that are sensitive clinical markers of specific language impairment (SLI). This has fuelled the theory that language impairment in autism represents a co-morbid SLI. However, the underlying cause of these deficits may be different in each disorder. In a novel task, we manipulated non-word stimuli in three ways known to influence the repetition accuracy of children with SLI. Participants with SLI were affected differently by these manipulations to children with autism. Children with autism performed similarly to language-matched typical children in terms of levels and patterns of performance, and types of error made, suggesting that the underlying cognitive cause of non-word repetition deficits is different in each disorder.