Loneliness is a negative emotional experience that can stem from a gap between desires and the reality of social relationships. It is also a predictor of mental health. Loneliness is therefore important to investigate in neurodevelopmental populations known for having difficulties in the social sphere. This co-registered study involved 48 youths with autism spectrum disorders (ASD), 54 youths with 22q11.2 deletion syndrome (22q11DS) and 65 typically developing youths (TD) aged 12-30. State loneliness was assessed with an ecological momentary assessment. Paper-pencil questionnaires assessing attitude toward aloneness, trait loneliness, and mental health, were completed by the youths and their caregivers. A comparable level of state loneliness between clinical groups and TD were found, with greater loneliness when alone than in a social context. Clinical groups showed a greater intra-individual variability. Both individuals with ASD and 22q11DS revealed a greater affinity toward being alone than TD, but only individuals with ASD reported greater trait loneliness. However, no significant association was found between attitude toward aloneness, trait and state loneliness. Emotional reactivity to loneliness was different between the clinical groups. Self-reported mental health only was associated with loneliness in the clinical groups. These results provide new insights into the understanding of loneliness in these clinical populations and have an impact on clinical care by highlighting the need to remain vigilant when encountering youths who report feeling lonely, and that these youths need to be supported in developing their social network, which appears to be a protective factor against loneliness.