御三時[osanji] three-o'clock snack
三鞭酒[shanpen] champagne
球面三角法[kyuumensankakuhou] spherical trigonometry
胸三寸[munesanzun] heart
元三[ganzan] New Year's period (January 1st to 3rd)

五十三次[gojuusantsugi] the 53 Toukaidou stages
向こう三軒[mukousangen] one's next three neighbors
降三世明王[gouzanzemyouou] Trailokyavijaya Vidya-raja
再三[saisan] again and again
再三再四[saisansaishi] repeatedly

杜父魚[tofugyo] sculpin (any fish of family Cottidae, inc. the bullheads and the miller's-thumb)
杜撰[zusan] careless
杜漏[zurou] careless
杜宇[hototogisu] lesser cuckoo (Cuculus poliocephalus)
杜夫魚[kakubutsu] fourspine sculpin (species of fish, Cottus kazika)

杜絶[tozetsu] stoppage
鎮守の杜[chinjunomori] grove of the village shrine
杜氏[touji] chief brewer at a sake brewery (after name of sake's alleged inventor)
杜若[kakitsubata] rabbitear iris (Iris laevigata)

田鵑[hototogisu] lesser cuckoo (Cuculus poliocephalus)
杜鵑草[hototogisu] toad lily (Tricyrtis hirta)

山杜鵑草[yamahototogisu] lesser cuckoo (Cuculus poliocephalus) (esp. one living in the mountains)
杜鵑花[tokenka] satsuki azalea (Rhododendron indicum)