The distribution of arabino-4-O-methylglucuronoxylans (AGXs) and O-acetyl-galactoglucomannans (GGMs) in warts and the warty layer of tracheids in normal wood (NW) and compression wood (CW) of Cryptomeria japonica was investigated. Under field emission scanning electron microscope (FE-SEM) observation, warts and the warty layer of delignified NW and CW tracheids were degraded by xylanase treatment, indicating that warts and the warty layer contain high amounts of AGXs. However, the effect of xylanase was not observed in NW and CW tracheids before delignification, suggesting that AGXs in warts and the warty layer may be encrusted with lignin. After ${eta}$-mannanase treatment, no noticeable changes were observed in warts and the warty layer of NW tracheids, indicating that warts and the warty layer contain either no or very few GGMs. Similar results to FE-SEM observations were also observed with immunogold labeling. AGX labeling was observed in warts and the warty layer of NW and CW tracheids, while GGM labeling was not detected. NW tracheids showed a much stronger density of AGX labeling than did CW tracheids in warts and the warty layer, indicating differences in the chemical compositions of warts and the warty layer between NW and CW tracheids.