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Abstract Background Certifying long-term sick leave and coordinating complex rehabilitation programs are essential activities of social insurance doctors. These doctors have a role in preventing the decreased work capacity of employees that may lead to leaving the labour market and the transition of these employees to other social insurance benefits, such as a work disability pension. Objectives Analysis of long-term sick leaves (over 183 days) to identify risk factors and population groups with low potential for work capacity rehabilitation. Method We conducted a cross-sectional study between September 2019 and September 2020. The information was collected from the National Institute of Medical Assessment and Work Capacity Rehabilitation Bucharest registers and the EXPMED application. The data were statistically analysed using PSPP software. Results The highest rehabilitation percentage was achieved in cases of traumatic injuries (73.17%), followed by musculoskeletal diseases (70.06%). We noticed lower recovery in cases of nervous system diseases (50.56%) and cardiovascular diseases (44.23%). In the group that summed up the other pathologies, the recovery percentage was 58.37%. People who regained their work capacity were significantly younger (mean age 47.87 y ± 8.93) than those who turned to other forms of social benefits, such as a disability pension or an old-age pension (mean age 53.16 y ± 8.43). Conclusion Most of the subjects (72%) regained their work capacity and did not need a disability pension. We identified the sociodemographic and morbidity characteristics of people on long-term sick leave along with target groups requiring intensive intervention measures.