: Glycogen storage disease (GSD) type Ib is a congenital disorder of glycogen metabolism that is associated with neutropenia, neutrophil and monocyte dysfunction, and an inflammatory bowel disease (IBD) that mimics a Crohn disease phenotype. The enteric microflora is implicated in the pathogenesis of IBD; however, its role in the development of GSD-associated IBD is unknown. Antibody reactivity to Saccharomyces cerevisiae antibodies (ASCA), Escherichia coli outer membrane porin C (anti-OmpC), and bacterial flagellin (anti-CBir1) have been associated with Crohn disease in the general population, but they have an undetermined association in children and adults with GSD-Ib. Our goal was to examine the association of ASCA, anti-OmpC, and anti-CBir1 with the clinical features of GSD-Ib enterocolitis. : A retrospective review identified 19 patients with GSD-Ib with or without a known diagnosis of enterocolitis. Radiographic, endoscopic, and serologic data were collected and assays for ASCA, anti-OmpC, and anti-CBir1 obtained. : Seven patients had combined radiographic, endoscopic, and histologic evidence of intestinal inflammation; the majority had ileocolonic involvement. Seventeen of 19 (89%) patients had elevated anti-CBir1 levels (6/7 in the IBD group and 11/12 in the no clinical evidence of IBD group). Thirteen of 19 (68%) had elevated anti-OmpC levels (5/7 in the IBD group and 8/12 in the no clinical evidence of IBD group). Eleven of 19 (58%) patients had elevated ASCA IgA levels (4/7 in the IBD group and 7/12 in the no clinical evidence of IBD group). : Nearly all of the patients with GSD-Ib had elevated anti-CBir1 levels. The antibody did not differentiate those with and without a diagnosis of GSD-Ib-associated IBD. Seroreactivity to flagellin may represent immune dysfunction rather than active enterocolitis in this patient population. Long-term follow-up of the group without known IBD is required to determine whether these antibodies can predict intestinal inflammation.