Until recently, intestinal metaplasia (IM) at the squamocolumnar junction (SCJ) was ascribed to Barrett's mucosa (BM), which arises from gastro-oesophageal reflux. Recent studies, however, have shown that IM at the SCJ can also be induced, for example, by Helicobacter pylori (HP). The aim of this study was to investigate whether the type of IM might be helpful in the differentiation between these two aetiologies. Biopsies from the antrum, corpus and immediately below the Z-line were taken from 443 patients. Eighty-three of them showed IM below the Z-line. In these, the endoscopic aspect of the Z-line was classified as either unremarkable (n=49) or suspected of BM (n=34). Typing of IM was done using Gomori's aldehyde fuchsin-Alcian blue staining. Overall, age, HP status and erosive oesophagitis had no influence on the IM type. Type-III IM (n=24) was more frequent in men (P=0.0371) and related to endoscopic BM (P<0.0001). Type-I/II IM (n=59) was associated with an unremarkable Z-line (P<0.0001) and was linked to multifocal gastric IM (P=0.016) and HP (P=0.0011). In conclusion, it was shown that, in the presence of a normal Z-line, especially in the absence of HP, type-III IM is suggestive of BM. The diagnosis of short or ultra-short segment BM should therefore include endoscopic, histological and histochemical characteristics.