We describe a 40-year-old woman with Salmonella cholecystitis complicating adult-onset X-linked chronic granulomatous disease (CGD) caused by a de novo mutation in the paternal-origin CYBB gene. CGD was diagnosed by familial genetic analysis of the CYBB gene encoding NADPH oxidase gp91phox after detection of a refractory subcutaneous abscess at the age of 28. At age 40, she began experiencing frequent fever and diarrhea over a period of 3 months that were refractory to antibacterial treatment. Cholecystitis was evident. Her symptoms improved after percutaneous trans-hepatic gallbladder aspiration puncture with stand-by cholecystectomy. Salmonella enterica serotype Enteritidis (S. Enteritidis) was detected in blood, stool, and bile acid samples. Due to her suppressed bactericidal ability caused by CGD, S. Enteritidis was considered to have translocated from the gut to reside in the gallbladder, causing her repeated enteritis and sepsis. When encountering CGD with recurrent salmonellosis, the possibility of cholecystitis should be considered as another infection focus.