The mouse and human Hox complex consists of 39 genes in four linkage groups (A-D). Although the structure and expression patterns of most of these genes have been reported, the 5' members of the Hox C linkage group have been only partially characterized. Herein we report the primary and genomic structure of the mouse Hoxc11 gene as well as its expression pattern. The Hoxc11 gene encodes a 304 amino acid protein which is translated from a 2.2 kb transcript, derived from two exons. Hoxc11 mRNA is found in the most posterior region of the developing embryo commencing at 9.5 days of gestation. Expression is detected in the posterior neural tube, dorsal root ganglia, prevertebrae and hindlimbs. Expression is also found in metanephric mesenchyme which, later in development, becomes restricted to the cortical region of the developing kidney. In the developing genitalia, prominent expression is first observed in the posterior urogenital sinus that gives rise to the urethra, vagina and prostate. Later, expression is seen in paramesonephric and mesonephric ducts and in the genital tubercle. In the hindlimbs, Hoxc11 expression is seen in the mesenchyme posterior to the region forming the femur and fibula, but does not extend anteriorly to the region giving rise to the tibia or distally to the tarsal bones.