The overlap between autism and Rett syndrome clinical features has led to many cases of Rett syndrome being initially diagnosed with infantile autism or as having some autistic features. Both conditions seriously disrupt social and language development and are often accompanied by repetitive, nonpurposeful stereotypic hand movements. The aims of this study were to compare the early and subsequent clinical courses of female subjects with Rett syndrome categorised by whether or not a diagnosis of autism had been proposed before Rett syndrome had been diagnosed and compare the spectrum of methyl-CpG binding protein 2 (MECP2) mutations identified among the two groups. This study made use of a total of 313 cases recorded in two databases: the Australian Rett Syndrome Database (ARSD) and the International Rett Syndrome Phenotype Database (InterRett). Cases with an initial diagnosis of autism had significantly milder Rett syndrome symptoms and were more likely to remain ambulant, to have some functional hand use and not to have developed a scoliosis. Females with the p.R306C or p.T158M mutations in the MECP2 gene were more likely to have an initial diagnosis of autism, and the specific Rett syndrome symptoms were noted at a later age. We recommend that females who are initially considered to have autism be carefully monitored for the evolution of the signs and symptoms of Rett syndrome.