The objective was to evaluate long-term transverse, anteroposterior and vertical skeletal changes after rapid maxillary expansion (RME). The data were clinical trials that assessed skeletal changes through cephalometric analysis. No surgical or other simultaneous treatment during the evaluation period was accepted. Electronic databases (PubMed, Medline, Medline In-Process & Other Non-Indexed Citations, Cochrane Database of Systematic Reviews, ASP Journal Club, DARE, CCTR, Embase, Web of Sciences and Lilacs) were searched with the help of a senior Health Sciences librarian. Abstracts that appeared to fulfill the initial selection criteria were selected by consensus. The original articles were then retrieved. A methodological checklist was used to evaluate the quality of the selected articles. Their references were also hand-searched for possible missing articles. Articles without an adequate control group to factor out growth changes were excluded. Only three articles (one measuring transverse and two anteroposterior and vertical changes) measured RME stability after active expansion, all of them had some methodological flaws, which limit the attainable conclusions. An individual analysis of these articles was made. Long-term transverse skeletal maxillary increase is approximately 25% of the total dental expansion for prepubertal adolescents. Better long-term outcomes are expected in transverse changes because of RME in less skeletally mature patients. RME appears not to produce clinically significant anteroposterior or vertical changes in the position of the maxilla and mandible. The conclusions from this systematic review should be considered with caution because only a secondary level of evidence was found. Long-term randomized clinical trials are needed.