The study reports measurements of radon and its decay products and of perceived air quality carried out in an occupied and unoccupied auditorium at the Lublin University of Technology in Lublin, Poland during three air conditioning system operation modes – air conditioning off, air conditioning on and air conditioning on/off. In the air conditioning on/off mode radon and its decay product concentrations and values of perceived air quality were inversely related. During that air conditioning operation mode, the value of the mean equilibrium factor F for the unattached fraction (0.31 ± 0.19) was somewhat higher than for the attached fraction (0.24 ± 0.19) and significant negative correlations were found between F values for attached, unattached and for the sum of both progeny fractions and perceived air quality values. These findings may be of importance as they indicate that in certain air conditioning operation modes indoor air quality deteriorates along with a reduction in the radon health hazard. This, in turn may adversely affect the comfort and productivity of the room users.