Objectives To identify diagnostic, patient/employee, general practitioner (GP) and practice factors associated with length of certified sickness episodes.

Methods Twelve-month collection of fit note data at 68 general practices in eight regions of England, Wales and Scotland between 2011 and 2013. Secondary analysis of sick note data collected at seven general practices in 2001/2002. All employed patients receiving at least one fit note at practices within the collection period were included in the study. Main study outcomes were certified sickness episodes lasting longer than 3, 6 and 12 weeks.

Results The data from seven practices contributing in 2013, and a decade previously, suggest that periods of long-term sickness absence may be falling overall (risk >12 weeks absence, OR=0.65) but the proportion of mild–moderate mental disorder-related (M-MMD) episodes is rising (26% to 38%). Over 32% (8064/25 078) of fit notes issued to working patients in the 68 practices were for a M-MMD. A total of 13 994 patient sickness ‘episodes’ were identified. Diagnostic category of episode, male patients, older patient age and higher social deprivation were significantly associated with the >3 week, >6 week and long-term (>12 week) outcomes, and GP partner status with the long-term outcome only.

Conclusions In the context of a rapidly changing legislative environment, the study used the largest sickness certification database constructed in the UK to enhance the evidence base relating to factors contributing to long-term work incapacity.