UK Biobank is an ambitious post-genomic project involving the recruitment and follow-up of 500 000 volunteers aged 45 to 69 years. Many primary care teams will be involved in the study directly or indirectly. The programme of research will use at least five data sources: paper-based questionnaires, blood samples, genotype information derived from the bloods, clinical/prescribing data from the medical records, and data on deaths. We describe three of the key challenges to primary care informatics posed by this project: patient recruitment, confidentiality, and data management. We then describe solutions proposed in Scotland, based on existing technologies. Some of these may be applicable elsewhere in the other Regional Collaborating Centres and other large-scale collaborative projects which rely on primary care informatics.