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Background Lung disease caused by exposure to chemical substances such as polyhexamethylene guanidine (PHMG) used in humidifier disinfectants (HDs) has been identified in Korea. Several researchers reported that exposure classification using a questionnaire might not correlate with the clinical severity classes determined through clinical diagnosis. It was asserted that the lack of correlation was due to misclassification in the exposure assessment due to recall bias. We identified the cause of uncertainty to recognize the limitations of differences between exposure assessment and clinical outcomes assumed to be true value. Therefore, it was intended to check the availability of survey using questionnaires and required to reduce misclassification error/bias in exposure assessment. Methods HDs exposure assessment was conducted as a face-to-face interview, using a questionnaire. A total of 5245 applicants participated in the exposure assessment survey. The questionnaire included information on sociodemographic and exposure characteristics such as the period, frequency, and daily usage amount of HDs. Based on clinical diagnosis, a 4 × 4 cross-tabulation of exposure and clinical classification was constructed. When the values of the exposure rating minus the clinical class were ≥ 2 and ≤ − 2, we assigned the cases to the overestimation and underestimation groups, respectively. Results The sex ratio was similar in the overestimation and underestimation groups. In terms of age, in the overestimation group, 90 subjects (24.7%) were under the age of 10, followed by 52 subjects (14.2%) in their 50s. In the underestimation group, 195 subjects (56.7%) were under the age of 10, followed by 80 subjects (23.3%) in their 30s. The overestimation group may have already recovered and responded excessively due to psychological anxiety or to receive compensation. However, relatively high mortality rates and surrogate responses observed among those under 10 years of age may have resulted in inaccurate exposure in the underestimation group. Conclusions HDs exposure assessment using a questionnaire might not correlate with adverse health effects due to recall bias and various other causes such as recovery of injury and psychological anxiety. This study revealed exposure misclassification and characteristics affected by HDs and proposed a questionnaire-based exposure assessment methodology to overcome the limitations of past exposure assessment.