Background Negative symptoms in schizophrenia are related to impaired functioning. The presence of negative symptoms in early phases of psychosis in individuals at clinical risk is receiving increased attention. Methods We evaluated comprehensively a sample of 92 young people (age range 15–25) applying the Clinical Assessment Interview for Negative Symptoms (CAINS), adapted for youth. Individuals at clinical high risk (CHR, n=29) were compared to individuals with schizophrenia (SZ, n=31) and normal controls (NC, n=32). In addition to the CAINS, participants were assessed with the Structured Interview for Prodromal Syndromes (SIPS), enabling examination of the relations among scales, as well as the Penn Computerized Neurocognitive Battery (CNB), to examine association with cognitive performance, and the Global Assessment of Function (GAF) to assess overall functioning. Results The CHR group was intermediate to SZ and NC on nearly all clinical measures. Negative symptoms on the CAINS correlated better with negative than with other symptoms on the SIPS and were associated with neurocognitive deficits and poorer functioning. Conclusions This study illustrates the feasibility of in-depth evaluation of negative symptoms in youth and indicates that these symptoms are present already in the at-risk state and relate to impaired cognition and functioning.