Objectives We investigated dampness/mold in schools and dwellings, and food habits and subjective symptoms in elementary school pupils, in order to clarify the effect of dampness and food habits on subjective symptoms in elementary school pupils. Methods Questionnaires were used to investigate dampness in classrooms and dwellings in Hokkaido, Japan, and its effect on subjective symptoms in 1,077 pupils in 8 elementary schools. We used a dampness index for both the home and classroom; the index was the sum of the presence of four dampness indicators: (1) visible mold, (2) moldy odor, (3) water leakage, and (4) condensation on windowpanes. The questionnaire also contained queries about food habits, as follows: the frequency of eating breakfast, whether the energy provided by the school lunch was sufficient, and whether eating too many snacks and/or sweets were consumed. Adjusted logistic regression was used to determine whether dampness and food habits were related to the subjective symptoms. Results In fully adjusted models, the home dampness index was significantly related to cough, general symptoms, and having at least one symptom; the classroom dampness index was significantly related to nasal symptoms. In addition, usually not eating breakfast was significantly related to eye symptoms, and too many snacks and/or sweets was significantly related to eye, nasal, and general symptoms. Conclusions Both home and classroom dampness can affect pupils' health. Home dampness, in particular, was significantly related to cough and general symptoms, and classroom dampness was significantly related to nasal symptoms. Furthermore, favorable food habits have a positive effect on pupils' subjective symptoms.