This article presents measurements of biological contaminants in two elementary schools that serve inner city minority populations. One of the schools is an older building; the other is newer and was designed to minimize indoor air quality problems. Measurements were obtained for airborne fungi, carpet loadings of dust mite allergens, cockroach allergens, cat allergens, and carpet fungi. Carbon dioxide concentrations, temperature, and relative humidity were also measured. Each of these measurements was made in five classrooms in each school over three seasons--fall, winter, and spring. We compared the indoor environments at the two schools and examined the variability in measured parameters between and within schools and across seasons. A fixed-effects, nested analysis was performed to determine the effect of school, season, and room-within-school, as well as CO2, temperature and relative humidity. The levels of all measured parameters were comparable for the two schools. Carpet culturable fungal concentrations and cat allergen levels in the newer school started and remained higher than in the older school over the study period. Cockroach allergen levels in some areas were very high in the newer school and declined over the study period to levels lower than the older school. Dust mite allergen and culturable fungal concentrations in both schools were relatively low compared with benchmark values. The daily averages for temperature and relative humidity frequently did not meet ASHRAE guidelines in either school, which suggests that proper HVAC and general building operation and maintenance procedures are at least as important as proper design and construction for adequate indoor air quality. The results show that for fungi and cat allergens, the school environment can be an important exposure source for children.