Irx1 and Irx2 are members of the murine Iroquois homeobox (Irx) gene family. In this study, we describe the dynamic expression pattern of these genes during limb development with a focus on digit formation. We further present a comparative expression analysis with Gli genes (Gli1, Gli2, Gli3). Gli1, Gli2, and Gli3 were suggested for candidate regulators of the Irx genes. The expression was studied between E11.5 and E14.5 when the digits are being formed. Irx1 and Irx2 reproduce the developmental program of the digits in time and space and the Irx1 provides an early and excellent marker for this process. Our analysis also indicates that the expression of Irx1, Gli1 and Irx2, Gli2 are relative to each other. In contrast, Gli3 exhibits a different expression pattern.