Objective: Our purpose was to obtain information about the correlation between workers' self-perceived health and physician-assessed functional limitations. We also studied whether this correlation differed between workers with subjective health complaints that cannot (SHC) and those that can be explained (non-SHC) by a well-defined medical disease. Methods: Baseline data of 2040 participants from a prospective cohort study were used for this study. These participants answered a questionnaire on their self-perceived health and received a medical work disability assessment during which physicians reported functional limitations. Pearson correlation analyses were used to calculate correlations between 4 functional limitation factors and 11 self-perceived health factors. For correlations with coefficients ≥0.30, linear regression analyses were performed to assess possible differences between participants with SHC (n = 363) and those with non-SHC (n = 1677). Results: We found correlations ≥0.30 between two functional limitation factors and six self-perceived health factors for all participants. SHC participants showed lower correlations than the non-SHC participants between the physical functional limitation and the SF-36 self-perceived physical health factors (−0.49, 95% CI −0.56 to −0.41 vs. -0.60, 95% CI -0.62 to −0.57) and between the mental functional limitation and the SF-36 self-perceived mental health factors (−0.30, 95% CI -0.39 to −0.20 vs. -0.40, 95% CI -0.44 to −0.36). Conclusion: Self-perceived health showed overall low to moderate correlations with physician-assessed functional limitations. Some of these correlations were lower for workers with SHC than for those with non-SHC. This may indicate that physicians rely slightly more on well-defined medical complaints within medical work disability assessments.