Objective To compare the differences in mucin-histochemistry and etiology of Barrett's esophagus (BE) intestinal metaplasia (IM) , cardiac intestinal metaplasia (CIM) and gastric antrum intestinal metaplasia (GA-IM). Methods Alcian blue /periodic acid-schiff (AB/PAS) and high iron diamine / alcian blue (HID/AB) histochemical methods were used to classify IM in BE, cardia and gastric antrum, and IM were classified into three subtypes: complete small intestinal type (type Ⅰ ) , incomplete small intestinal type (type Ⅱ) and incomplete colonic type (type Ⅲ). Compared the prevalence of different subtypes of IM in above-mentioned sites, and investigated their relationships among the symptoms of gastroesophageal reflux disease (GERD) and Helicobacter pylori (Hp) infection. Results The prevalence of type Ⅲ IM in long-segment BE (LSBE) and short-segment BE (SSBE) is 75. 0% and 63. 3% respectively, it is significantly higher than that in CIM (23. 1% ) and GA-IM ( 17. 7% ) (P 0. 01 ). The positive rates of the symptoms of GERD in LSBE, SSBE, CIM and GA-IM are 78. 6% , 76. 7% , 42. 3% and 17. 7% respectively , and the former three are significantly higher than the latter one (P 0. 01). The positive rates of Hp infection in LSBE (17. 9% ) and SSBE (20. 0% ) are significantly lower than those in CIM (46. 2% ) and GA-IM (64. 7% ) (P 0. 01). Conclusion The subtypes of IM in LSBE and SSBE are type 1 predominantly , but there are low incidence of type 3333 in CIM and GA-IM. LSBE and SSBE are significantly associated with GERD, and aren't with Hp infection. However, CIM and GA-IM are mainly related to Hp infection, while GERD probably participates to the pathogenesis of CIM.