To study the clinical, epidemiological, and microbiological associations between intestinal failure (IF) and central line-associated infections (CLABSI) in patients with central vein catheters (CVCs) during 2005-2016. We compared retrospectively CLABSI rates according to background disease, type of line access, pathogen distribution, and antibiotic susceptibilities. One hundred and fourteen children (64.1% < 4 years) were enrolled. Main diagnoses were persistent diarrhea (20, 17.5%), short bowel syndrome (13, 11.4%), continuous-TPN w/o diarrhea (11, 9.7%), very early-onset inflammatory bowel disease (VEO-IBD, 8, 7%), Hirschsprung's disease (3, 2.6%), non-oncologic hematologic conditions (13, 11.4%), and other diseases (46, 40.4%). 152.749 catheter days were recorded; 71.1% had Hickman's catheters. Two hundred and nine CLABSI episodes were recorded in 58 patients (82% with IF, 13.7 and 8.2/1000 catheter days in IF, and non-gastrointestinal conditions, P = 0.09). More CLABSI were recorded in continuous TPN vs. VEO-IBD or persistent diarrhea (38.8 vs.15.8 and 12.8/1000 catheter days, P < 0.004). Among patients with Hickman in jugular vein, highest CLBSI incidence was in continuous TPN, VEO-IBD, and persistent diarrhea (29.9, 15.84, and 12.49 episodes/1000 catheter days, respectively). CVCs were removed in 38.8% CLABSI. Two hundred and thirty-five pathogens were isolated (Enterobacteriaceae spp. in 39% of IF patients, mostly in persistent diarrhea and short bowel syndrome patients, 47.6% and 34.8%, respectively). Coagulase-negative Staphylococcus was the commonest pathogen in continuous TPN, VEO-IBD, and Hirschsprung's (71.4%, 55.6% and 46.1%, respectively). CLABSI rates in IF patients were among the highest reported. We reported a "hierarchy" in CLABSI incidence among patients with IF and showed that CLABSI incidence and etiology were different as function of background diseases and CVC insertion site.