© 2014. Background: Chromosome 22q11.2 deletion syndrome (22q11.2DS) is a complex genetic disorder with a variable clinical presentation that can include cardiac, neural, immunological, and psychological issues. Previous studies have measured elevated anxiety and depression in children with 22q11.2DS. Comorbity of anxiety and depression is well established in the pediatric literature but the nature of comorbidity patterns has not been empirically established in children with 22q11.2DS. Comorbidity of anxiety and depression has important implications for treatment and prognosis, and may be a marker of risk in this population of children at high-risk for developing schizophrenia. Method: Participants were 131 boys and girls ages 8-14 with (n=76) and without (n=55) 22q11.2DS and their mothers. Children and mothers independently completed self- and parent-report measures of anxiety and depression. Mothers also completed measures of behavioral functioning including the Behavioral Assessment for Children, 2nd ed. (BASC-2). Cluster analyses were conducted to test if theoretically based groupings of anxiety and depression could be identified. We hypothesized four psychological profiles based on child- and mother-reports: low/no anxiety and low/no depression, higher depression and low/no anxiety, higher anxiety and no/low depression, and a comorbid profile of higher anxiety and higher depression. BASC-2 subscale scores were then compared across subgroups of children to determine if a comorbid profile would predict greater behavioral difficulties. Results: In the full sample of children both with and without 22q11.2DS, cluster analyses of self and maternal reported anxiety and depression revealed the expected subgroups: (1) a group of children with higher anxiety/lower depression (anxious); (2) a group with primary depression (lower anxiety/higher depression (depressed)); (3) a comorbid group with higher anxiety/higher depression (comorbid); and, (4) a lowest anxiety/lowest depression group (NP). Mothers' reports produced highly similar groupings. Furthermore, the 22q11.2DS youth were more likely to be in anxiety, depressed or comorbid clusters than the typically developing (TD) youth. Children with 22q11.2DS comorbid for anxiety and depression exhibited the worst functional outcomes (e.g., poor poorer functional communication, and reduced daily life activities). Conclusions: Anxiety, comorbid with depression may be of particular concern in children with 22q11.2DS who arguably carry a greater burden on their stress coping resources than children without a complex genetic disorder. Furthermore, the manifestation of negative mood, anxiety and difficult behavior is likely to reverberate between the child and her or his environment. This can lead to negative interactions with family, peers, and teachers, which in turn further taxes coping resources. Comorbidity of anxiety and depression within a vulnerable population highlights the need for the development of tailored interventions.