The oral hygiene and oral status of children with severe disabilities with both nutritional and respiratory complications who were institutionalized at Karugamonoie (KNI), a facility for children with disabilities, were investigated in this study. Their oral hygiene management was solely dependent on caregivers and nurses at the institution. Thirty children (13 females, 17 males; average age, 7.6 years) who had a tracheotomy and feeding tube (gastrostomy, nasogastric, or jejunostomy feeding tube) were included in the study. As for oral characteristics, poor control of tongue movement, anterior open-bite, abnormal strain of facial muscles, dry mouth, and swallowing dysfunction were found in 63.3%, 63.3%, 13.3%, 20.0%, and 100.0%, of the children, respectively. The mean ± standard deviation Decayed, Missing, Filled Teeth score was 0.13 ± 0.57. The Gingival Index (GI) showed that the children had mild (53.3%) to moderate (46.7%) gingivitis. The Simplified Oral Hygiene Index was excellent in 50.0% of the children, good in 23.3%, fair in 20.0%, and poor in 6.7% of the children. These indices were satisfactory in general except for GI management, which may have been hampered by abnormal oral functions and anterior open-bite. In conclusion, oral hygiene management of children with nutritional and respiratory complications at KNI was shown to be of high quality even without on-site intervention by dental specialists.