Comorbidity is common among long-term sick-listed and many prognostic factors for return to work (RTW) are shared across diagnoses. RTW interventions have small effects, possibly due to being averaged across heterogeneous samples. Identifying subgroups based on prognostic RTW factors independent of diagnoses might help stratify interventions. The aim of this study was to identify and describe subgroups of long-term sick-listed workers, independent of diagnoses, based on prognostic factors for RTW. Latent class analysis of 532 workers sick-listed for eight weeks was used to identify subgroups based on seven prognostic RTW factors (self-reported health, anxiety and depressive symptoms, pain, self-efficacy, work ability, RTW expectations) and four covariates (age, gender, education, physical work). Four classes were identified: Class 1 (45% of participants) was characterized by favorable scores on the prognostic factors; Class 2 (22%) by high anxiety and depressive symptoms, younger age and higher education; Class 3 (16%) by overall poor scores including high pain levels; Class 4 (17%) by physical work and lack of workplace adjustments. Class 2 included more individuals with a psychological diagnosis, while diagnoses were distributed more proportionate to the sample in the other classes. The identified classes illustrate common subgroups of RTW prognosis among long-term sick-listed individuals largely independent of diagnosis. These classes could in the future assist RTW services to provide appropriate type and extent of follow-up, however more research is needed to validate the class structure and examine how these classes predict outcomes and respond to interventions.