Background: Although incidence data for work-related ill-health in the UK are available, more detailed information for smaller geographical areas has hitherto been unpublished. Aims: To estimate the incidence of work-related ill-health reported by clinical specialists in Scotland, 2002-2003. Methods: THOR (The Health and Occupation Reporting network) is a UK wide reporting scheme for work-related ill-health. In 2002-2003, 241 out of 2162 physicians in THOR were based in Scotland. We have summarized the reported cases and calculated incidence rates for categories of ill-health by age, gender and industry. The UK Labour Force Survey (2002) was used to provide denominator data, with comparisons made between rates for Scotland and the rest of the UK. Results: In 2002-2003, 4043 estimated cases were reported from Scotland. Mental ill-health was most frequently reported (41%); followed by musculoskeletal disorders (31%), skin disorders (16%), respiratory disease (10%), hearing disorders (2%) and infection (1%). The reported average annual incidence rate per 100 000 employees for all work-related ill-health in Scotland was 86.0. The highest reported rate for mental ill-health was found for employees in public administration and defence (76.7 per 100 000), and health and social work (72.3 per 100 000). The construction industry had the highest reported rate of musculoskeletal disorders (41.6 per 100 000), while hairdressers appeared at most risk of developing occupational contact dermatitis (rate=86.4 per 100 000). Conclusions: Despite its limitations, THOR has indicated types of work-related ill-health and related industries for targeted disease prevention in Scotland. © The Author 2005. Published by Oxford University Press on behalf of the Society of Occupational Medicine. All rights reserved.