Hereditary congenital facial paresis (HCFP) belongs to the family of congenital cranial dysinnervation disorders and is characterized by an isolated dysfunction of the facial nerve (nVII). While genetic defects have been identified for several members of this disease family, genes underlying congenital facial paresis and Möbius syndrome remain to be discovered. Here we focus on HCFP linked to chromosome 3q21-q22 and identify new candidate genes using expression analysis by means of RNA in situ hybridization during mouse embryogenesis. We selected 28 positional candidates and identified 17 genes with undetectable expression levels during mouse development, ubiquitous expression, or expression in tissues not affected in HCFP. Additionally, 7 genes were excluded by direct sequence or reverse transcription-PCR analysis. The remaining 4 genes (Klf15, Flj40083, Kiaa0779, and Podxl2) were found to be expressed at spatial and temporal positions during mouse development that correlate with HCFP regions in humans, defining these genes as primary candidates in HCFP.