The concentration levels of particulate matter (PM), airborne fungi, carbon dioxide as well as temperature and relative humidity were investigated in the indoor and outdoor environment of two schools in Athens, Greece during the period January to May 2011. The overall concentration ranges of the indoor measured pollutants were: PM10: 14.92-166.18 μg/m3, PM2.5: 3.16-31.27 μg/m3, PM1: 0.72-9.01 μg/m3, UFP: 4188-63093 pt/cm3, total airborne fungi: 28-2098 CFU/m3 and CO2: 389-1717 ppm. The relationships between PM and airborne fungi were mainly examined, and bivariate correlations of all the measured environmental parameters are also reported. The results indicate that PM of certain aerodynamic diameters significantly correlate to the total airborne fungi and their prevalent genera, Penicillium, Cladosporium and Aspergillus. Principal Component Analysis (PCA) was conducted so as to cluster variables of common characteristics. Furthermore, simple and multiple linear regression models were developed to investigate several cases of dependent variables to be used for prediction purposes in health risk assessments.