Objective To explore the impacts of NPHP1 knockdown on the phenotype of Madin-Darby canine kidney (MDCK) cells. Methods The expression of NPHP1 in MDCK cells was knockdown by siRNA interference. Cells were divided into normal control group, negative control group and siRNA group. The cellular morphology and migration were observed by light microscope. The mRNA expressions and activities of matrix metalloproteinases 2 and 9 (MMP2 and MMP9) were detected by real time PCR and gelatin zymography. The mRNA and protein expressions of E-cadherin, β-catenin, zonula occluden-1 (ZO-1), ZO-1-associated nucleic acid binding protein (ZONAB) and α-smooth muscle actin (α-SMA) were analyzed by real time PCR, Western blotting and immunocytochemistry. Results Compared with those in normal control group, in siRNA group the mRNA expressions of E-cadherin, β-catenin and ZO-1 decreased, and MMP9, MMP2, α-SMA and ZONAB increased after interfering NPHP124 h (all P<0.05); the protein expressions of E-cadherin,β-catenin and ZO-1 decreased and ZONAB and α-SMA increased after 48 h (all P<0.05), and MDCK cells became elongated with enhanced migration capacity; siRNA cells had decreased expressions of E-cadherin and β-catenin on the membrane, but increased expression of ZONAB in cytoplasm and nucleoplasm after 72 h, and α-SMA was also observed in some interfered cells. Conclusions NPHP1 knockdown induces epithelial-mesenchymal transition in MDCK cells, and ZO-1/ZONAB signaling pathway was activated. These changes may associate with renal interstitial fibrosis of Nephronophthisis type I.