Background: Long-term sickness absence results in increased risks of permanent disability and a compromised quality of life. Return to work is an important factor in reducing these risks. Little is known about return to work factors for long-term sick-listed workers with subjective health complaints. The aim of this study was to evaluate prognostic factors for partial or full return to a paid job for at least 28 days for long-term sick-listed workers with subjective health complaints, and to compare these factors with those of workers with other disorders. Methods: Data from a prospective cohort study of 213 participants with subjective health complaints and 1.037 reference participants were used. The participants answered a questionnaire after 84 weeks of sickness absence. Return to work was measured after one and two years. Univariable logistic regression analyses were performed (P ≤ 0.157) for variables per domain with return to work (i.e. demographic, socio-economic and work-related, health-related, and self-perceived ability). Subsequently, multivariable logistic regression analyses with backward selection (P ≤ 0.157) were performed. Remaining factors were combined in a multivariable and final model (P ≤ 0.05). Results: Both for workers with subjective health complaints and for the reference group, non-health-related factors remained statistically significant in the final model. This included receiving a partial or complete work disability benefit (partial: OR 0.62, 95% CI 0.26-1.47 and OR 0.69, 95% CI 0.43-1.12; complete: OR 0.24, 95% CI 0.10-0.58 and OR 0.12, 95% CI 0.07-0.20) and having a positive self-perceived possibility for return to work (OR 1.06, 95% CI 1.01-1.11 and OR 1.08, 95% CI 1.05-1.11). Conclusions: Non-health-related factors seem to be more important than health-related factors in predicting return to work after long-term sickness absence. Receiving a work disability benefit and having negative expectations for return to work seem to complicate return to work most for workers with subjective health complaints. With respect to return to work predictors, workers with subjective health complaints do not differ from the reference group.