Chlorophyll a fluorescence parameters and photosynthetic pigments content in leaves of broccoli (Brassica oleracea L. var. italica) cv. ‘Monaco’ F1 and cauliflower (Brassica oleracea L. var. botrytis) cv. ‘Bruce’ F1 transplants were analyzed to investigate the effects of chilling temperatures (6 and 10 °C) and the exposure length (1 or 2 weeks) on the photosynthetic apparatus condition in 3-year experiment. Data were compared to control plants exposed to 14 °C for 1 and 2 weeks. The lowest values of maximum quantum efficiency of photosystem II (Fv/Fm) and the performance index (PI) were observed in cauliflower chilled at 6 °C for 2 weeks. This was not accompanied by any substantial reduction in chlorophylls concentration, however, significant correlations between Fv/Fm or PI and chlorophylls content in cauliflower leaves were found. There was no negative effects of chilling on photosynthetic activity and chlorophyll content in broccoli leaves, the amount of carotenoids significantly increased in the broccoli chilled for 2 weeks in 6 °C. The chlorophyll a fluorescence indices and accelerated carotenoids synthesis showed that broccoli had less vulnerable photosynthetic apparatus to stress-induced temperatures and more efficient protection mechanisms in comparison to cauliflower transplants.