The measurement of variable chlorophyll (Chl) a fluorescence is widely used as a convenient and versatile tool in photosynthesis research. In many applications empirical correlations and simplified models of Chl a fluorescence are used with success. Nevertheless, variable Chl a fluorescence provides only indirect and complex image of processes occurring within photosynthetic membranes and such simplifications have only limited validity. In this review we elucidate some controversial and still unresolved questions about the origin and interpretation of the variable Chl a fluorescence induction and the proper use of variable Chl a fluorescence for studies of photochemical events in photosystem 2 (PS2). Although the major part of variable Chl a fluorescence reflects the photochemical closure of the PS2 reaction centers (RCs) and can be considered as a function of the redox state of the primary acceptor QA, up to 50 % of the change in the Chl a fluorescence yield can be of secondary, nonphotochemical origin. We review the possible sources of the inherent heterogeneity in the origin of variable Chl a fluorescence. We also comment on the practical implications this bears for the use of variable Chl a fluorescence. and G. Samson, O. Prášil, B. Yaakoubd.