Cux-1 is a murine homeobox gene that is highly and transiently expressed in the developing kidney. To further evaluate the role of Cux-1 in mammalian kidney development, organotypic cultures of embryonic mouse kidney were incubated with phosphorothioate-coupled antisense Cux-1 oligonucleotides (ODNs) in the presence of cationic liposomes. Inhibition of Cux-1 expression by antisense ODNs was verified by reverse transcription-PCR. Metanephroi that were incubated with antisense Cux-1 ODNs were 23% smaller than metanephroi that were incubated with sense Cux-1 ODNs. Morphologic analysis of metanephroi that were treated with antisense Cux-1 ODNs revealed that ureteric buds and induced epithelial structures were present. However, extensive areas of cell death containing shrunken cells with pyknotic nuclei were also evident. The presence of increased apoptosis was verified by ultrastructural and terminal transferase-mediated dUTP nick end labeling analyses. Two different antisense Cux-1 ODNs targeting either the translation start codon or the homeobox produced increased apoptosis. In contrast, metanephroi incubated with sense ODNs exhibited only occasional apoptotic cells. We conclude that the presence of antisense Cux-1 ODNs does not block nephron induction, but results instead in increased apoptosis. Proper regulation of Cux-1 expression may be necessary for normal kidney development.