Selective participation in biobanks often compromises inference to the general population, particularly when selection occurs across multiple stages, whether at recruitment or during subsequent participation. Inverse probability (IP) weighting can reduce systematic differences using suitable external benchmarks, but most applications assume a single selection process. Here, we present a multi-stage IP-weighting framework and apply it to the Danish Blood Donor Study (DBDS), a nationwide biobank embedded in Denmark’s blood-donation infrastructure. Using national registers, we estimated year-specific probabilities of (i) donation activity and (ii) DBDS enrolment conditional on donation activity, yielding two-stage inclusion weights for 169,893 participants. These weights reduced inclusion-associated imbalance across the 52 auxiliary variables in the probability models by 97.6% (median) and, despite strong health selection under donation-based recruitment, reduced relative-prevalence discrepancies across held-out prescription phenotypes by 69.7% (median). The effective sample size after weighting was 30,627 (18.0% of 169,893). Combining the inclusion weights with questionnaire-specific response weights across five DBDS questionnaires (>500 questions) produced the largest changes from unweighted to weighted responses for health behaviours and symptom severity, including tobacco and alcohol consumption, menstrual-pain severity, restless-legs severity, nocturia, sleep disturbance, and fatigue. These findings support multi-stage IP-weighting to improve population alignment in biobanks with staged selection.

The authors have declared no competing interest.

This study was supported by a grant from the Independent Research Fund Denmark. The Danish Blood Donor Study (DBDS) is funded by an annual grant from Bio- and Genome Bank Denmark. The initiation of DBDS was supported by the Danish Administrative Regions (02/2611) and the Danish Council for Independent Research (09-069412). Additionally, DBDS is funded by the Novo Nordisk Foundation (NNF23OC0082015, NNF17OC0027864, and NNF17OC0027594). T.F.H. is funded by the Lundbeck Foundation (R507-2025-275).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

DBDS was approved by the Central Denmark (1-10-72-95-13) and Zealand (SJ-740) Regional Committees on Health Research Ethics and the Data Protection Agency (P-2019-99). Oral and written informed consent was obtained from all DBDS participants. All methods were carried out in accordance with the relevant guidelines and regulations (including the Declaration of Helsinki).

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

Person-level data from DBDS needed to reproduce this study cannot be made publicly available due to confidentiality legislation. Furthermore, this study is based on pseudonymized register data located on a secure platform at Statistics Denmark. Meta-data and programs are available from the authors upon reasonable request and with permission of the DBDS steering committee, the Ethical Committee, and the Danish Data Protection Agency. Enquiries about legal possibilities for accessing these data within DBDS, scripts/codes and further information should be addressed to the corresponding author.