Although an association between chilling tolerance and aquaporins has been reported, the exact mechanisms involved in this relationship remain unclear. We compared the expression profiles of aquaporin genes between a chilling-tolerant and a low temperature-sensitive rice variety using real-time PCR and identified seven genes that closely correlated with chilling tolerance. Chemical treatment experiments, by which rice plants were induced to lose their chilling tolerance, implicated the PIP1 (plasma membrane intrinsic protein 1) subfamily member genes in chilling tolerance. Of these members, changes in expression of the OsPIP1;3 gene suggested this to be the most closely related to chilling tolerance. Although OsPIP1;3 showed a much lower water permeability than members of the OsPIP2 family, OsPIP1;3 enhanced the water permeability of OsPIP2;2 and OsPIP2;4 when co-expressed with either of these proteins in oocytes. Transgenic rice plants (OE1) overexpressing OsPIP1;3 showed an enhanced level of chilling tolerance and the ability to maintain high OsPIP1;3 expression levels under low temperature treatment, similar to that of chilling-tolerant rice plants. We assume that OsPIP1;3, constitutively overexpressed in the leaf and root of transgenic OE1 plants, interacts with members of the OsPIP2 subfamily, thereby improving the plants' water balance under low temperatures and resulting in the observed chilling tolerance of the plants.