To study the role of MADS-box genes in developing apples (Malus ×domestica Borkh.), clones corresponding to seven different genes, MdMADS5 to MdMADS11, were isolated from a 2-day-old apple cDNA library. Through DNA sequence comparison, six genes were classified into the APETALA1 (AP1) group and one gene, MdMADS10, into the AGAMOUS (AG) group. Six of the genes, MdMADS5 to MdMADS10, were found to be preferentially expressed in fruit following pollination. These genes also showed differential expression patterns in core, cortex and skin of young fruit. For instance, MdMADS5, which is highly homologous to AP1, showed preferential expression in the cortex and skin tissues while MdMADS10, which is highly homologous to AGL11, showed exclusive expression in the core tissues. The gene MdMADS11 showed a similar expression level and pattern in flowers, fruit at several early developmental stages, and for different fruit tissues. The range of expression patterns suggests that the genes play different roles in apple development.