Background. In 1998, Denmark introduced the flex job scheme to ensure employment of people with a permanent reduced work capacity. This study investigated the association between select diagnoses and the risk of disability pension among persons eligible for the scheme. Methods. Using the national DREAM database we identified all persons eligible for the flex job scheme from 2001 to 2008. This information piece was linked to the hospital discharge registry. Selected participants were followed for 5 years. Results. From the 72,629 persons identified, our study included 329 patients with rheumatoid arthritis, 10,120 patients with spine disorders, 2179 patients with ischemic heart disease, and 1765 patients with functional disorders. A reduced risk of disability pension was found in the group with rheumatoid arthritis (hazard ratio = 0.69 (0.53-0.90)) compared to the group with spine disorders. No differences were found when comparing ischemic heart disease and functional disorders. Employment during the first 3 months of the flex job scheme increased the degree of employment for all groups. Conclusion. Differences in the risk of disability pension were identified only in patients with rheumatoid arthritis. This study demonstrates the importance of obtaining employment immediately after allocation to the flex job scheme, regardless of diagnosis.