DAF-19, the only RFX transcription factor found in C. elegans, is required for the formation of neuronal sensory cilia. Four isoforms of the DAF-19 protein have been reported, and the m86 nonsense (null) mutation affecting all four isoforms has been shown to prevent cilia formation. Transcriptome analyses employing microarrays of L1 and adult stage worms were completed using RNA from daf-19(m86) worms and an isogenic wild type strain to identify additional putative DAF-19 target genes. Using transcriptional fusions with GFP, we compared the expression patterns of several potential gene targets using fluorescence confocal microscopy. Expression patterns were characterized in various genetic backgrounds in order to determine isoform-specific expression patterns. Additionally, we completed rescue experiments using cDNAs encoding specific DAF-19 isoforms in a daf-19 null genetic background. Our data indicate that at least five new genes are activated and four new genes are repressed by DAF-19 in both ciliated and non-ciliated neurons. Few of these genes are known to contain a classical X-box motif through which DAF-19 gene regulation is thought to occur. We are currently developing isoform-specific CRISPR/Cas9 mutants to further explore the precise mechanisms by which different DAF-19 isoforms regulate their target genes.