Here we report on the severe defects in renal epithelium induced by the transgenic Col2-Cre line used previously for skeletal tissue-specific gene targeting. We demonstrate that conditional ablation of the Kif3a or Pkd1 genes encoding primary cilium/intraflagellar transport-associated proteins using type II collagen-specific Cre transgenic strain results in a severe form of polycystic kidney disease in mice. We detect Col2-Cre recombinase expression in kidney epithelium, which reflects expression of the endogenous Col1alpha(II) gene in the embryonic renal tubules. We determine the exon 2-containing splice variant of the Col1alpha(II) gene as a major transcript expressed in kidney. Furthermore, the confocal immunocytochemical analysis demonstrates deposition of the type II collagen within the mesenchymal-epithelial renal tissue interfaces and its co-localization with the basement membrane marker collagen IV during embryonic kidney morphogenesis.