The Forkhead box transcription factors, Foxc1 and Foxc2, are crucial for development of the eye, cardiovascular network, and other physiological systems, but their cell‐type specific and postdevelopmental functions are unknown, in part because conventional (i.e., whole‐organism) homozygous‐null mutations of either factor result in perinatal death. Here, we describe the generation of mice with conditional‐null Foxc1^flox and Foxc2^flox mutations that are induced via Cre‐mediated recombination. Mice homozygous for the unrecombined alleles are viable and fertile, indicating that the conditional alleles retain their wild‐type function. The embryos of Foxc1^flox or Foxc2^flox mice crossed with Cre‐deleter mice that are homozygous for the recombined allele (i.e., Foxc1^Δ/Δ or Foxc2^Δ/Δ embryos) lack expression of the corresponding gene and show the same developmental defects observed in conventional homozygous mutant embryos. We expect these conditional mutations to enable characterization of the cell‐type specific functions of Foxc1 and Foxc2 in development, disease, and adult animals. genesis 50:766–774, 2012. © 2012 Wiley Periodicals, Inc.