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Psychiatric problems are common in autism spectrum disorders (ASDs), but the reasons are poorly understood. We use a longitudinal population-representative cohort to examine for the first time the persistence of psychiatric problems and to identify risk factors for their occurrence and stability.Eighty-one 16-year olds (75 male, six female), initially seen at 12 years, were re-assessed using the parent-report Strengths and Difficulties Questionnaire (SDQ). Child, family and contextual characteristics from age 12 were tested as risk factors for psychopathology.Prevalence rates varied depending on whether general population or ASD-specific SDQ cut-offs were used. While the former suggested a decrease in psychiatric problems over time, the ASD-specific cut-offs showed no significant differences. With the exception of ADHD, the ASD-specific cut-offs identified a smaller proportion of individuals as ‘affected’ than did the general population cut-offs. There was longitudinal domain specificity, with parent correlations ranging from 0.50 to 0.58 and teacher SDQ reports at age 12 correlating 0.33–0.53 with parent reports at 16 years. In examining the role of risk factors, lower IQ and adaptive functioning predicted higher hyperactivity and total difficulties scores. Greater emotional problems at 16 were predicted by poorer maternal mental health, family-based deprivation and lower social class. Improvement from 12 to 16 years in conduct problems was predicted by greater neighbourhood deprivation and special school attendance.This is the first longitudinal study of other psychiatric symptoms in ASD. Additional psychiatric problems in ASD are persistent and domain-specific from childhood to adolescence. The finding that age-related reduction in SDQ symptoms does not apply when ASD-specific cut-offs are used requires further evaluation using diagnostic measures. Only a few of the expected risk factor-psychopathology predictions expected from general population studies were found, raising the possibility that the causes of psychopathology in ASD differ from those in the general population.