Quantification of chlorophyll (Chl) fluorescence is a versatile tool for analysing the photosynthetic performance of plants in a non-intrusive manner. A pulse-amplitude modulated fluorometer was combined with a CNC router for the automated measurement of the effective quantum yield of photosystem 2 (Φ2) of Arabidopsis thaliana plants. About 90 000 individual plants representing 7 500 lines derived from En-transposon and T-DNA mutagenised Arabidopsis populations were screened for mutants with altered Φ2. Forty-eight recessive Φ2 mutations were identified of which most exhibit also altered pigmentation and increased photosensitivity. For three Φ2 mutants the corresponding mutated genes were identified that code all for chloroplast-located proteins. Comparison of the Φ2 mutant screen with other screening methods based on the measurement of Chl fluorescence shows that the Φ2 mutants identified are different to mutants identified by high Chl fluorescence. Some Φ2 mutants, on the contrary, are common to mutants identified by screens based on non-photochemical quenching. and C. Varotto ... [et al.].