To understand the factors affecting the incidence of blossom-end rot (BER), the effect of the Ca/K ratio (4/12–12/4, in me·L–1) in nutrient solutions and Ca concentration in fractions in the distal part of young tomato fruits immediately before BER symptoms appear were investigated for three seasons. The rate of BER incidence increased with a decrease in the Ca/K ratio in the supplied solutions in the summer and spring, but little difference was observed in the winter. Ca concentration was highest in winter and lowest in summer, and the concentration in fractions decreased with a decrease in the Ca/K ratio of the solutions. When the results of all three experiments were pooled, among the fractions, water-soluble Ca concentration was found to have the highest significance in the relationship to BER incidence. The risk of BER incidence in rapidly growing tomato increased to a critical level when water-soluble Ca in the distal part of the fresh fruit decreased to less than 0.20 μmol·g–1 FW. Multiple-regression analysis revealed that the concentration of water-soluble Ca, which is predominantly recovering apoplastic or cytoplasmic Ca2+, and total Ca, which has been translocated during fruit development, are significantly affected by solar radiation and Ca concentration in the supplied solution rather than air temperature.