A series of indoor air quality parameters were determined in two medieval churches, in Cyprus (temperature, relative humidity, total and UV solar radiation, CO2 indoors and O3, NO, NO2*, HNO3*, HCl, HCOOH, CH3COOH indoors and outdoors). These data were used as input in a validated indoor air quality model to predict indoor air pollutant source strengths and species concentrations that resulted from dark or photochemical reactions. The NO and NO2 emission rates due to the burning of incense or candles were estimated. Model results revealed that heterogeneous NO formation takes place simultaneously with the heterogeneous HONO formation. Also, model application has shown that indoor NOx emissions resulted in decreased free radical concentrations, in contrast to the organic compound emissions, which increased free radical concentrations. This effect of indoor emissions on indoor radicals can partly explain the indoor enhancement/depression of indoor gaseous acid formation.