Comparisons of ambient (outdoor) airborne fungal populations to indoor populations are frequently employed when assessing air quality. Ground-level samples are collected as reference values during these comparisons, despite the location of the building's air intakes at heights above the ground. To judge the validity of this practice, contemporaneous ground-level and air intake (rooftop) bioaerosol samples were collected at buildings in the Midwest. The samples were obtained using Anderson N-6 single-stage samplers and cultured on Rose Bengal agar. Viable fungi, including non-sporulating organisms, were identified and reported as colony-forming units per cubic meter of air (CFU/m3). A two-tailed Student-t was used to test the difference between paired ground-level and rooftop, loge-transformed concentrations (n=26). The mean difference between paired values was found to be significant (p <0.001) with rooftop concentrations ranging between 13 to 94 percent of their ground-level counterpart. In addition to the quantitative variation, no pair of contemporaneous samples was found to contain identical taxa. Nonparametric tests of the paired samples indicate that the rank order of taxa found in the ground-level samples do not agree with the ranking found in the rooftop samples. The results suggest that ground-level airborne populations are not reliable predictors of the number, type, or order of fungi found in the air near rooftop intakes.