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Fruit morphogenesis is a process unique to the angiosperms, and yet little is known about its developmental control. Following fertilization, fruits typically undergo a dramatic enlargement that is accompanied by differentiation of numerous distinct cell types. To identify genes putatively involved in the early development of grapevine fruit, we used the fleshless berry mutant (Vitis vinifera L. cv Ugni Blanc) that has dramatically reduced fruit size due to a lack of pericarp development. Using oligo-specific arrays, 53 and 50 genes were identified as being down- and up-regulated, respectively, in the mutant. In parallel, Suppression Subtractive Hybridization performed between the mutant and the wild type (WT) allowed the identification of new transcripts differentially expressed during the first stages of mutant and WT pericarp development. From this data, the picture emerged that the mutation promotes the expression of several genes related to ripening and/or to stress and impairs the expression of several regulatory genes. Among those, five genes encoding proteins previously reported to be associated with, or involved in, developmental processes in other species (a specific tissue protein 2, ATHB13, a BURP domain protein, PISTILLATA, and YABBY2), were identified and investigated further using real-time PCR and in situ hybridization. Expression in the pericarp was confirmed, specific spatial and/or temporal patterns were detected and differences were observed between the WT and the mutant during fruit development. Expression of these genes appeared to be affected during young fruit development in the mutant, suggesting that they may play a role in grape berry morphogenesis.