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Background  In contrast to aetiological associations, there is little empirical evidence for generalising health service use associations from cohort studies. We compared the health service use of cohort study participants diagnosed with bowel or lung cancer to the source population of people diagnosed with these cancers in New South Wales (NSW), Australia to assess the representativeness of health service use of the cohort study participants.    Methods  Population-based cancer registry data for NSW residents aged ≥45 years at diagnosis of bowel or lung cancer were linked to the 45 and Up Study, a NSW population-based cohort study (N~ 267,000). We measured hospitalisation, emergency department (ED) attendance and all-cause survival, and risk factor associations with these outcomes using administrative data for cohort study participants and the source population. We assessed bias in prevalence and risk factor associations using ratios of relative frequency (RRF) and relative odds ratios (ROR), respectively.    Results  People from major cities, non-English speaking countries and with comorbidites were under-represented among cohort study participants diagnosed with bowel ( n  = 1837) or lung ( n  = 969) cancer by 20–50%. Cohort study participants had similar hospitalisation and ED attendance compared with the source population. One-year survival after major surgical resection was similar, but cohort study participants had up to 25% higher post-diagnosis survival (lung cancer 3-year survival: RRF = 1.24, 95% confidence interval 1.12,1.37). Except for area-based socioeconomic position, risk factors associations with health service use measures and survival appeared relatively unbiased.    Conclusions  Absolute measures of health service use and risk factor associations in a non-representative sample showed little evidence of bias. Non-comparability of risk factor measures of cohort study participants and non-participants, such as area-based socioeconomic position, may bias estimates of risk factor associations. Primary and outpatient care outcomes may be more vulnerable to bias.    Electronic supplementary material  The online version of this article (10.1186/s12874-018-0537-3) contains supplementary material, which is available to authorized users.

Self-selection in a population-based cohort study: impact on health service use and survival for bowel and lung cancer assessed using data linkage