The risk of intussusception related to percutaneous endoscopic gastrostomy with jejunal extension (PEG-J) in patients with severe motor and intellectual disabilities (SMID) remains unknown. In a cross-sectional study, a review of 26 patients (mean age, 11.6 ± 6.4 years) with SMID who underwent PEG-J was performed. During the follow-up period, 6 of 26 (23%) patients developed intussusception. The median period from PEG-J to the onset of intussusception was 364 (range, 8–1344) days. No significant difference was observed in the Cobb angle between the intussusception and nonintussusception groups; however, body mass index at the time of PEG-J was significantly lower in the intussusception group. Intussusception related to PEG-J occurs relatively frequently in patients, and it is possibly attributable to factors such as deformity caused by undernutrition and weight loss. If enteral nutrition via PEG-J has been established, earlier enterostomy can be recommended because of the high risk of intussusception in patients with SMID.