Superficial flat early carcinomas of the gallbladder are rarely detected clinically. We previously reported that these carcinomas display granular, flat, or gastric area-like surface mucosal patterns. However, these patterns are also seen in some non-neoplastic conditions. To more definitively differentiate carcinomas from non-neoplastic lesions, we analyzed the stereomicroscopic structure of macroscopically granular, flat, or gastric area-like mucosal lesions with a methylene-blue contrast technique. Sixteen superficial flat early carcinomas and 65 non-neoplastic flat lesions from surgically resected gallbladders were studied by stereomicroscopy. The fine mucosal structures were classified into three patterns: grooved, pitted, or papillary, each of which was further subdivided into regular and irregular. The frequency of the grooved (52.2%) and papillary (52.2%) patterns was significantly higher in the carcinomas than in the non-neoplastic lesions (24.7% and 1.3%, respectively). The pitted pattern was present in 69.6% of the carcinomas and in 53.2% of the non-neoplastic lesions (the difference was not significant). In the grooved and pitted patterns, the irregular subtypes predominated in the carcinomas (100% and 81.3%, respectively), while the regular subtypes were more frequent in the non-neoplastic lesions (84.2% and 97.6%, respectively). Stereomicroscopic examination of the fine mucosal structures of flat lesions of the gallbladder is very useful in differentiating carcinomas from non-neoplastic lesions.