Abstract: Objective To determine symptom overlaps between functional heartburn (FH), functional dyspepsia (FD), and irritable bowel syndrome (IBS). Methods One hundred and ten patients with frequent heartburn but no mucosa breakage under endoscopy were enrolled consecutively. They were required to fill out a questionnaire. The overlapped symptoms of FD and IBS symptoms were screened using Rome Ⅲ criteria. The participants were also examined using Hamilton anxiety scale/Hamilton depression scale. All of the participants were followed with 24 h esophageal multichannel intra-luminal impedance monitoring with pH sensor (MII-pH) monitoring and proton pump inhibitor (PPI) trials. The participants were divided into non-erosive reflux disease (NERD) and FH groups. The prevalence of symptom overlaps FD and IBS, between NERD and FH groups was analyzed. Results Women were more likely to present with FH than with NERD (P<0.05). The participants with FH had higher prevalence of anxiety and depression than those with NERD (92% vs. 75%，88% vs. 65% respectively，P<0.05). Fifty-two (47.3%) patients with heartburn symptom had FD symptoms; 31 (28.2%) had IBS symptoms, and 10 (9.09%) had both FD and IBS symptoms. Patients with FH were more likely to have symptom overlaps of FD and IBS than those with NERD (62% vs. 35%, 48% vs.11.7%, respectively; P<0.01). Epigastric pain syndrome (EPS), a subtype of FD, was slightly more likely to have overlapped NERD and FH symptoms than postprandial discomfort symdrome (PDS). But the difference was not significant (29.1% vs. 18.2%, P>0.05). IBS-diarrhea was also slightly more likely to have overlapped NERD and FH symptoms than IBS-constipation. Again, the difference was not significant (16.4% vs. 11.8%, P>0.05). Conclusion Female, higher prevalence of anxiety and depression, overlapped FD and IBS symptoms are more likely to appear in FH patients than in NERD patients.