Introduction Decreasing participation levels in health surveys pose a threat to the validity of estimates intended to be representative of their target population. If participants and non-participants differ systematically, the results may be biased. The application of traditional non-response adjustment methods, such as weighting, can fail to correct for such biases, as estimates are typically based on the sociodemographic information available. Therefore, a dedicated methodology to infer on non-participants offers advancement by employing survey data linked to administrative health records, with reference to data on the general population. We aim to validate such a methodology in a register-based setting, where individual-level data on participants and non-participants are available, taking alcohol consumption estimation as the exemplar focus. Methods and analysis We made use of the selected sample of the Health 2000 survey conducted in Finland and a separate register-based sample of the contemporaneous population, with follow-up until 2012. Finland has nationally representative administrative and health registers available for individual-level record linkage to the Health 2000 survey participants and invited non-participants, and the population sample. By comparing the population sample and the participants, synthetic observations representing the non-participants may be generated, as per the developed methodology. We can compare the distribution of the synthetic non-participants with the true distribution from the register data. Multiple imputation was then used to estimate alcohol consumption based on both the actual and synthetic data for non-participants, and the estimates can be compared to evaluate the methodology's performance. Ethics and dissemination Ethical approval and access to the Health 2000 survey data and data from administrative and health registers have been given by the Health 2000 Scientific Advisory Board, Statistics Finland and the National Institute for Health and Welfare. The outputs will include two publications in public health and statistical methodology journals and conference presentations. © 2019 Author(s) (or their employer(s)).