Cell fate determination is tightly controlled by the expression of transcription factors and gene regulatory networks. PAX6 is a transcription factor containing a DNA-binding paired-box domain and homeobox domain that plays a key role in the development of the eye, brain, and pancreas. Here, we showed that histone deacetyltransferase 1 (HDAC1) is a novel binding partner of PAX6 in newborn mouse retinas. We also showed that HDAC1 specifically binds to the paired and transactivation domains of PAX6, and these physical interactions were required for effective repression of PAX6 transcriptional activity during retinal development. Furthermore, HDAC1 preferentially regulates the transcriptional activity of PAX6 when it binds to paired-domain (P6CON and chimeric pCON/P3) PAX6 responsive elements compared to homeodomain (pP3) PAX6 responsive elements. The repressive effect of HDAC1 on the transcriptional activity of PAX6 was reversed by knockdown of HDAC1 or treatment with an HDAC inhibitor, TSA. Taken together, these results show that HDAC1 binds PAX6 and that protein-protein interaction leads to transcriptional repression of PAX6 target genes during mouse retinal development. (C) 2016 Elsevier Inc. All rights reserved.