Individuals with Rett syndrome (RTT) can have variable manifestations of stereotypies. In this nation‐wide cross‐sectional study, we recruited all individuals with RTT in Taiwan diagnosed as RTT by neurologists based on genetic findings and diagnostic criteria. The data were collected using questionnaire. A total 43 cases of typical RTT and 15 cases of atypical RTT, aged from 2.1 to 40.1 years, were enrolled. They included 3 (5.2%) in stage II, 42 (72.4%) in stage III, and 13 (22.4%) in stage IV. All individuals presented with at least one stereotypy. Individuals with atypical RTT had more varied stereotypies (mean: 14 ± 6) compared to those with typical RTT (mean: 9 ± 5) (P = 0.003). Flapping (73.3%) and wringing (58.1%) were the most common hand stereotypies in atypical and typical RTT, respectively. Compared with typical RTT, hair pulling, bruxism, retropulsion, and protrusion of lips were more common in atypical RTT (P = 0.003, P = 0.006, P = 0.003 and <0.001, respectively). The number of stereotypies did not differ among different stages, clinical severities, and hand functions. Although there were no age‐related changes in stereotypies in atypical RTT, flapping (P = 0.012), clapping (P = 0.044), and mouthing with single hand (P = 0.009) were significantly more prevalent in individuals aged <10 years with typical RTT, and they decreased after 10 years. In conclusion, our study showed that the stereotypical movements varied in typical and atypical RTT, implying the heterogeneous nature of the disease and the pathogenic mechanisms of RTT with atypical features. Autism Res 2017. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. Autism Res 2017, 10: 1204–1214. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.