Background: Differentiated minute submucosal cancers ≤ 3 cm that exhibit no lymphovascular invasion are considered eligible for endoscopic resection; however, the ≤ 3 cm criterion remains debatable. The aim of this study was to verify the optimal tumor size cutoff for endoscopic resection eligibility, and to determine whether two-dimensional tumor size measurement would be more accurate for this purpose. Methods: The clinicopathological data of 574 patients undergoing curative surgery for differentiated minute submucosal cancer were reviewed retrospectively. A receiver operating curve analysis and bootstrapped samples were used to identify the optimal cutoff values for predicting lymph node (LN) metastasis. Results: Four hundred fourteen patients were eligible for the study.LN metastasis accompanied 2.5% of differentiated minute submucosal cancers that were ≤ 3 cm in size and lacked lymphovascular invasion. There was no lymph node metastasis in the tumors with 1D sizes ≤ 1.0 cm and 2D sizes ≤ 1.0 cm². Using 10,000 bootstrapped data, optimal cutoff values were 2.9 cm (LN metastasis: 2.1%) and 8.3 cm² (LN metastasis: 2.5% incidence) for one- and two-dimensional tumor size, respectively. Although the area under the curve was 0.611 (P = 0.046) for two-dimensional size, specificity and accuracy were greater for the dichotomized two-dimensional measure than for the dichotomized one-dimensional measure (P< 0.001, McNemar’s test). In addition, two-dimensional tumor size was the only significant risk factor for LN metastasis (odds ratio 1.09, 95% confidence interval 1.01–1.20). Conclusions: One-and two-dimensional cutoff values of 2.9 cm and 8.3 cm² might be suitable for patients at high risk of post-operative morbidity and mortality. Two-dimensional tumor size is an acceptable measurement method for estimating the risk of LN metastasis.