The in vivo variable fluorescence of chlorophyll a is used as a non-intrusive probe of the physiological state of intact leaves. It was established that the origin of this signal is the antenna system of photosystem II (PSII). The PSII population is heterogeneous with respect to antenna size, connectivity, electron transport activity, and localization. In this paper we have simulated the effect of these heterogeneities on the fluorescence transient using a mathematical model based on the redox reactions from the acceptor side of PSII. We have concluded that the systems with heterogeneous antenna size and connectivity can be simulated acceptably with a homogeneous population of PSII centres having average values for antenna size and the connectivity constant C. However, this is not possible if there are inactive PSII centres in the system (the so-called non-Q_B active centres). Finally, we have presented some possible applications of these types of simulations.