Inflammatory bowel disease is a chronic, relapsing-remitting gastrointestinal disorder which has become a serious global concern, and it imposes a great degree of health and economic burdens on communities worldwide. Although the presence of non-Helicobacter pylori Helicobacter (NHPH) microorganisms has been reported in various gastrointestinal disorders, their putative role in the pathogenesis of IBD has been a matter of controversy. The present study aimed to investigate the existence of gastric and enterohepatic NHPHs and their probable coinfection with H. pylori in IBD. Totally, 168 clinical specimens including 70 colonic biopsies and 98 fecal specimens were obtained from IBD patients. Genomic DNA was extracted from all samples, and its quality and concentration were assessed by β-globin PCR and spectrophotometry. The Helicobacter genus-specific PCR was performed using 16S rRNA gene. All samples were also tested for H. pylori infection by PCR of ureC gene fragment (glmM). The presence of NHPH was examined by using species-specific PCR assays. Based on PCR results, H. pylori was detected in 12.9% and 3.1% of colonic biopsies and fecal specimens, respectively. However, no statistically significant correlation was observed (P value > 0.05). We failed to find NHPH in both colonic biopsies and fecal specimens from IBD patients. Despite the fact that none of the IBD patients harbored the NHPH in the current work, further cohorts with larger sample size are required to determine the possible relationship between NHPH infection and IBD pathogenesis.