Chicken ovalbumin upstream promoter transcription factor-interacting proteins 1 and 2 (CTIP1 and CTIP2) are related transcriptional regulatory proteins. While overexpression of both of these proteins has been linked to the development of several lymphoid malignancies, lack of CTIP1 and CTIP2 expression results in defective lymphopoiesis and abnormal thymocyte development, respectively. Here, we describe the expression patterns of CTIP1 and CTIP2 during mouse embryogenesis and in the post-natal brain. Both CTIP1 and CTIP2 were expressed diffusely in the embryo at 10.5 days post-coitum (d.p.c.). However, the expression of both genes became increasingly restricted to the central nervous system (CNS) during the course of fetal development, culminating with high, but differential, expression levels throughout the hippocampal subregions, olfactory bulb and cortex, limbic system, basal ganglia and frontal cortex of the developing brain, and in dorsal cells of the spinal cord. The brain expression domains of CTIP1 and CTIP2 were maintained into adulthood. Outside the CNS, both genes exhibited differential expression within the facial mesenchyme at 12.5 d.p.c., and CTIP2 was selectively expressed from day 12.5 onwards in the olfactory epithelium and developing thymus, and to a lesser extent in oral and gut epithelia. Strong CTIP2 expression was maintained in the thymus at 18.5 d.p.c. These results support the selective contributions of both CTIP1 and CTIP2 in the development and function of both the central nervous and immune systems and the importance of future investigations to define the function(s) of both proteins.