22q11.2 deletion syndrome (22q11DS) has a complex phenotype with more than 180 characteristics, including cardiac anomalies, cleft palate, intellectual disabilities, a typical facial morphology, and mental health problems. However, the variable phenotype makes it difficult to predict clinical outcome, such as the high prevalence of psychosis among adults with 22q11DS (∼25–30% vs. ∼1% in the general population). The purpose of this study was to investigate whether subtypes exist among people with 22q11DS, with a similar phenotype and an increased risk of developing mental health problems. Physical, cognitive and behavioural data from 50 children and adolescents with 22q11DS were included in a k-means cluster analysis. Two distinct phenotypes were identified: Type-1 presented with a more severe phenotype including significantly impaired verbal memory, lower intellectual and academic ability, as well as statistically significant reduced total brain volume. In addition, we identified a trend effect for reduced temporal grey matter. Type-1 also presented with autism-spectrum traits, whereas Type-2 could be described as having more 22q11DS-typical face morphology, being predominately affected by executive function deficits, but otherwise being relatively high functioning with regard to cognition and behaviour. The confirmation of well-defined subtypes in 22q11DS can lead to better prognostic information enabling early identification of people with 22q11DS at high risk of psychiatric disorders. The identification of subtypes in a group of people with a relatively homogenous genetic deletion such as 22q11DS is also valuable to understand clinical outcomes.