The spatial and temporal patterning of sequence specific transcription factors (SSTFs) contributes to cell type specification and organ formation during embryogenesis. Homeodomain transcription factors are evolutionally conserved among invertebrate and vertebrate animals. They are responsible for body segmentation and organogenesis. Lbx1 and Pitx2 both are homeodomain transcription factors contributing to SSTF pattern formation during multiple organ formations. We studied how homeodomain transcription factors regulate SSTF and non-SSTF genes in a population-specific manner using the Lbx1[superscript EGFP] and Pitx2[superscript LacZ] mouse models. We have studied the role of Lbx1 in dorsal horn interneuron specification and Pitx2 in forelimb muscle formation. The two top non-SSTF target genes, NPY and Chmp2b, of Lbx1 are studied for expression pattern and potential neuronal function in neural tube. The T box, Hox gene families and Pax genes were identified as Pitx2 target genes via microarray analysis and their expression pattern were analyzed in forelimb. The expression domains of signaling molecules were altered in absence of Pitx2, suggesting that Pitx2 played a general role in pattern formation in forelimb mesenchyme.