Background Self-reported work-related ill-health (WRI) statistics suggest that agricultural workers in the UK are at an increased risk of musculoskeletal disorders (MSD), skin and respiratory disease. However, there is little comprehensive medically reported information on WRI in the UK agricultural sector. Methods Cases of WRI within the UK from 2002 to 2008, as reported to The Health and Occupation Reporting (THOR) network by occupational physicians, clinical specialists and general practitioners, were analysed. Directly standardized incidence rate ratios (SRRs) for the agricultural sector versus all other sectors were calculated for dermatological, musculoskeletal, respiratory and psychological illness, using as the standard population the UK working population as estimated from the Labour Force Survey. Results During 2002-08, 471 cases within the agricultural sector were reported to THOR (2% of all cases). Based on reports by clinical specialists, male agricultural workers aged <65 years had significantly raised SRRs for MSD (2.3, 95% CI 1.6-3.3), allergic alveolitis (32, 95% CI 19-51), asthma (1.9, 95% CI 1.2-3.0) and skin neoplasia (7.9, 95% CI 5.8-10.9) and a significantly reduced SRR for asbestos-related respiratory disease (0.4, 95% CI 0.2-0.7). Reports of mental ill-health in agricultural workers were low. Conclusions These medically reported incidence data provide information on WRI in the UK agricultural sector. Consistent with other sources, there are increased risks for asthma, allergic alveolitis and MSD and a reduced risk for mental ill-health. The raised incidence of skin cancer requires confirmation and further comparison with reliable estimates of the incidence in the UK workforce.