We investigated about the microbial concentrations of both the drain and the coil surfaces in the FCU for the building air-conditioning system. In this study, it was, considered that the microbial concentrations of the coil surface were a good index for the length tendency of the period using the FCU. The bacterial concentrations in drain water were same tendency, too. The coil surface of the smelling FCU had the higher microbial concentrations than the non-smelling FCU. In the case that the fungus concentrations of the coil surface between the smelling FCU and the non-smelling FCU were same level, the fungus concentrations of the drain water in the smelling FCU was high, and over 1,000 CFU/ml. The fungi, such as Cryptococcus albidus, Penicillium lilactinum, Sporobolomyces salmonicolor and Rhodotorula mucilaginasa in the FCU, were isolated. As one of causes of the smell, it was indicated that the fungi increased in the drain water of the FCU.