The Chronic Conditions Short Questionnaire (CCSQ) included as an optional package in the Health Behaviour in School-aged Children (HBSC) study protocol identifies adolescents with chronic conditions, and helps to understand the psychosocial impact of such illnesses. However, reliability of the results depends on the proper definition of the group with chronic conditions. The aim of this paper is to report on the validity of self-reported data on chronic conditions obtained from the CCSQ questionnaire used in a large school-based population study. Material and methods: The data was obtained from the 2010 HBSC study conducted in Poland in a group of 4570 pupils aged 13-17. The CCSQ includes three questions about chronic illness or disabilities occurrence diagnosed by a physician, and its selected consequences (missing school classes, medication). Four complex continuous scales were used as validation modules: the subjective complaints checklist and three sub-scales from the abbreviated Child Health and Illness Profile (CHIP-AE) questionnaire. The oldest age group was additionally asked about functional difficulties in: seeing, hearing, speaking, moving and breathing. Analysis of Variance with the post hoc test was used to compare subgroups of students defined according to CCSQ and functional difficulties. Results: Chronic conditions were reported by 20.3% of young respondents (95% confidence interval 19.2-21.5%). A statistically significant difference was found between the mean indexes of all validation scales when comparing healthy and chronically-ill students meeting criteria of CCSQ. The difference increases in comparison with chronically-ill students with functional difficulties, missing classes or taking medication. Conclusions: The CCSQ questionnaire is an appropriate tool for assessing the occurrence of long-term health problems from the perspective of adolescents. The instrument also importantly allows for an assessment of the impact of chronic and long-term conditions on medication usage and hindered access to education. Occurrence of long-term health problems is a significant confounding variable that should be routinely included in school surveys on health and health behaviours.