In a previous study, we demonstrated that Trps1-deficient (KO) mice show an expanded renal interstitium compared to wild-type (WT) mice because the loss of Trps1 affects the mesenchymal-epithelial transition (MET) in the cap mesenchyme and ureteric bud (UB) branching. Although we previously elucidated the mechanism underlying the impact of Trps1 on the MET, how Trps1 is involved in UB branching remains unknown. In the present study, we unveil the molecular mechanisms by which the loss of Trps1 suppresses UB branching. When we compared gene expression patterns via DNA microarray analysis using cultured ureteric buds isolated from E11.5 kidneys of WT and KO embryos, we found aberrant expression of genes associated with the transforming growth factor (TGF)-β/Smad3 signaling pathway in the KO UBs. Western blot and immunohistochemistry analyses showed increased levels of Rb1cc1, Arkadia1, and phosphorylated Smad3 and decreased levels of Smurf2, Smad7, and c-Ski in the KO embryonic kidneys. In addition, TUNEL staining and immunohistochemical detection of PCNA revealed that the apoptosis of UB cells was upregulated and, conversely, that cell proliferation was suppressed. Finally, we demonstrated that the suppression of UB branching in the KO UBs was restored via the exogenous addition of the Smad3 inhibitor SIS3, whereas the addition of TGF-β1 accelerated the suppression of UB branching in organ cultures of both isolated UBs and whole embryonic kidneys. Considering these results, we conclude that UB branching is suppressed through increased activation of the TGF-β/Smad3 signaling pathway when Trps1 is lost.