Calcium (Ca2+) concentration, early fruit growth, and expression of Ca2+-movement-related genes were analyzed during early fruit development in the tomato, which is the most important stage regarding the incidence of blossom-end rot (BER), to investigate the physiological mechanisms affecting the occurrence of BER. We used tomato introgression line IL8-3 with a chromosome segment from a wild relative (Solanum pennellii) because this line shows lower incidence of BER compared with the parent cultivar 'M82' (S. lycopersicum), as described previously. Ca2+ concentration in fruit and leaves was higher in IL8-3 than in 'M82', whereas no significant differences were observed between Ca2+ concentration in roots and stems of 'M82' and IL8-3. These results suggested that a Ca2+ transport property is an essential factor for the lower incidence of BER in IL8-3. IL8-3 fruit showed a lower growth rate than 'M82', which could result in preventing the occurrence of BER. The expression of genes encoding cation exchangers, Ca2+-ATPases, a Ca2+ channel, and Na+/Ca2+ exchangers, was higher in IL8-3 fruit than in 'M82' fruit, suggesting active Ca2+ movement in IL8-3. All results in this study could be related to physiological mechanisms accounting for the lower incidence of BER in IL8-3.