In this study, we aim to propose the optimal operation method of an earth-to-air heat exchanger (EAHE). As a first step, in this paper, we investigated the relationship between the occurrence of condensation and air pollution by fungi in the underground air tunnel of an actual building. Firstly, we evaluated of condensation in the underground air tunnel based on actual measurement and unsteady CFD analysis. Secondly, exhaustive investigation of fungal flora in the underground air tunnel was conducted by DNA analysis.