The objective of this study was to examine agreement between self-reported and medically recorded self-harm, and investigate whether the prevalence of self-harm differs in questionnaire responders vs. non-responders. A total of 4,810 participants from the Avon Longitudinal Study of Parents and Children (ALSPAC) completed a self-harm questionnaire at age 16 years. Data from consenting participants were linked to medical records (number available for analyses ranges from 205–3,027). The prevalence of self-harm leading to hospital admission was somewhat higher in questionnaire non-responders than responders (2.0 vs. 1.2%). Hospital attendance with self-harm was under-reported on the questionnaire. One third reported self-harm inconsistently over time; inconsistent reporters were less likely to have depression and fewer had self-harmed with suicidal intent. Self-harm prevalence estimates derived from self-report may be underestimated; more accurate figures may come from combining data from multiple sources.