Background Agriculture is one of the most physically demanding and risky industries. Aim The objective of this study was to provide baseline data on the diagnoses, occurrence and duration of sick leave of self‐employed Dutch farmers. Method A database of 22 807 sick leave claims of 12 627 farmers during the period 1994–2001 was analysed. Results Most of the claims (61%) were for musculo‐skeletal injuries and disorders. The mean cumulative incidence (CI) was 10.2 claims per year per 100 farmers and did not change over time. However, it varied per agricultural sector and per age category, being lowest in arable farming and in the youngest age category and highest in mushroom farming and in the oldest age category. The duration of sick leave depended both on diagnosis and age category: the slowest recovery from sick leave was seen in farmers with respiratory diseases and farmers in the oldest age category. Conclusion The results make it easier to identify groups of farmers to be targeted to prevent sick leave. To reduce the occurrence of sick leave in agriculture, the strategy should be to prevent musculo‐skeletal injuries and disorders. Furthermore, a sector‐specific approach is recommended, so that preventive actions can be focused on working conditions—specifically on workload and work safety. Efforts to shorten the duration of sick leave will also be valuable to obtain a reduction of sick leave.