The general principles involved in chlorophyll fluorescence quenching analysis by the saturation pulse method are presented, outlining the rationale for using the empirical fluorescence parameters F-v/F-m and Delta F/F-m' as indices for the photosystem II (PSII) photochemical quantum yield, Phi(II), in the dark-adapted or illuminated states, respectively. The relationship between Phi(II) and the quantum yield of photosynthetic electron transport is linear over a wide range of quantum flux densities. However, there is a fraction of PSII contributing approximately 30% to maximal quantum yield, which is closed at rather low quantum flux densities, while at the same time there is only a small drop in Delta F/F-m'. The details of F-m and F-m' determination by application of saturating light are critically examined, with emphasis on the situation in algae where the fluorescence rise to the peak level is followed by a rapid decline. For this purpose, the rapid induction kinetics upon onset of strong continuous illumination are investigated. Dark-adapted samples show two distinct intermediate fluorescence levels, I-1 and I-2, in the polyphasic rise from the O to the P level. The I-1 level separates a biphasic 'photochemical' rise, which also can be induced by a saturating single turnover flash, from several 'thermal' phases, induction of which requires multiple turnovers at PSII. Arguments are put forward favouring the I-2 level for assessment of F-m or F-m', on which calculation of F-v/F-m or Delta F/F-m' is based. It is shown that although an assessment based on the I-1 level, as practised by the so-called pump-and-probe method, does lead to a consistent underestimation of Delta F/F-m', in many cases similar information as with 12 determination is obtained.