Objectives Reliable retrospective exposure assessment continues to be a challenge in most population-based studies. Several methodologies exist for estimating exposures retrospectively, of which case-by-case expert assessment and job-exposure matrices (JEMs) are commonly used. This study evaluated the reliability of exposure estimates for selected carcinogens obtained through three JEMs by comparing the estimates with case-by-case expert assessment within the Netherlands Cohort Study (NLCS). Methods The NLCS includes 58 279 men aged 55–69 years at enrolment in 1986. For a subcohort of these men (n=1630), expert assessment is available for exposure to asbestos, polycyclic aromatic hydrocarbons (PAHs) and welding fumes. Reliability of the different JEMs (DOMJEM (asbestos, PAHs), FINJEM (asbestos, PAHs and welding fumes) and Asbestos JEM (asbestos) was determined by assessing the agreement between these JEMs and the expert assessment. Results Expert assessment revealed the lowest prevalence of exposure for all three exposures (asbestos 9.3%; PAHs 5.3%; welding fumes 11.7%). The DOMJEM showed the highest level of agreement with the expert assessment for asbestos and PAHs (κs=0.29 and 0.42, respectively), closely followed by the FINJEM. For welding fumes, concordance between the expert assessment and FINJEM was high (κ=0.70). The Asbestos JEM showed poor agreement with the expert asbestos assessment (κ=0.10). Conclusions This study shows case-by-case expert assessment to result in the lowest prevalence of occupational exposure in the NLCS. Furthermore, the DOMJEM and FINJEM proved to be rather similar in agreement when compared with the expert assessment. The Asbestos JEM appeared to be less appropriate for use in the NLCS.