Preoperative　neoadjuvant　chemoradiation　therapy　may　be　useful　in　patients　with　operable　rectal　cancer,　but　treatment　responses　are　variable.　We　examined　whether　expression　levels　of　circadian　clock　genes　could　be　used　as　biomarkers　to　predict　treatment　response.　We　retrospectively　analyzed　clinical　data　from　250　patients　with　rectal　cancer,　treated　with　neoadjuvant　chemoradiation　therapy　in　a　single　institute　between　2011　and　2013.　Gene　expression　analysis　(RT-PCR)　was　performed　in　tissue　samples　from　20　patients　showing　pathological　complete　regression　(pCR)　and　20　showing　non-pCR.　The　genes　analyzed　included　six　core　clock　genes　(Clock,　Per1,　Per2,　Cry1,　Cry2　and　Bmal1)　and　three　downstream　target　genes　(Wee1,　Chk2　and　c-Myc).　Patient　responses　were　analyzed　through　contrast-enhanced　pelvic　MRI　and　endorectal　ultrasound,　and　verified　by　histological　assessment.　pCR　was　defined　histologically　as　an　absence　of　tumor　cells.　Among　the　250　included　patients,　70.8%　showed　regression　of　tumor　size,　and　18%　showed　pCR.　Clock,　Cry2　and　Per2　expressions　were　significantly　higher　in　the　pCR　group　than　in　the　non-　pCR　group　(P＜0.05),　whereas　Per1,　Cry1　and　Bmal1　expressions　did　not　differ　significantly　between　groups.　Among　the　downstream　genes　involved　in　cell　cycle　regulation,　c-Myc　showed　significantly　higher　expression　in　the　pCR　group　(P＜0.05),　whereas　Wee1　and　Chk2　expression　did　not　differ　significantly　between　groups.　Circadian　genes　are　potential　biomarkers　for　predicting　whether　a　patient　with　rectal　cancer　would　benefit　from　neoadjuvant　chemoradiation　therapy.