Arabidopsis AtPPD2 encodes a ZIM-domain containing protein that acts as a negative regulator in cell proliferation. We show here that over-expression of AtPPD2 in tomato plants led not only to the significant reduction in size of cotyledons and developing leaves during vegetative growth phase, but also to the altered architecture of mature compound leaves through inhibition of cell division and expansion. Interestingly, the constitutive expression of AtPPD2 in transgenic tomato plants resulted in the growth inhibition of roots, suggesting that AtPPD2 is also a potential repressor for root cell proliferation. In Addition, over-expressing AtPPD2 caused a significant reduction in fruit and seed size. We noted that the transgenic fruits had a thinner pericarp layer, suggesting an additional role of AtPPD2 in carpel cell division and expansion prior to ripening. The expression levels of cell proliferation marker genes in the leaves and flower buds of transgenic tomato plants such as LeCYCD3;1, LeCYCB2;1 and LeCDKB2;1 were markedly reduced. Taken together, these results indicate that AtPPD2 functionally acts as a negative regulator during vegetative and reproductive growth and development in transgenic tomato plants through repression of cell cycle-related gene expression. Our results also demonstrate the potential usefulness of AtPPD2 gene in modulating fruit and seed setting processes in vegetable crop plants.