BackgroundThe relationship between pathological factors and lymph node metastasis of pathological stage early gastric cancer has been extensively investigated. By contrast, the relationship between preoperative factors and lymph node metastasis of clinical stage early gastric cancer has not been investigated. The present study was to investigate discrepancies between preoperative and postoperative values.MethodsFrom January 2011 to December 2013, 1042 patients with clinical stage early gastric cancer who underwent gastrectomy with lymphadenectomy were enrolled. Preoperative and postoperative values were collected for subsequent analysis. Receiver operating characteristics curves were computed using independent predictive factors.ResultsSeveral discrepancies were observed between preoperative and postoperative values, including existence of ulcer, gross type, and histology (all McNemar p-values were <0.001). Multivariate analyses identified the following independent predictive factors for lymph node metastasis: postoperative values including age (p = 0.002), tumor size (p < 0.001), and tumor depth (p < 0.001); preoperative values including age (p = 0.017), existence of ulcer (p = 0.037), tumor size (p = 0.009), and prediction of the presence of lymph node metastasis in computed tomography scans (p = 0.002). These postoperative and preoperative independent predictive factors produced areas under the receiver operating characteristics curves of 0.824 and 0.660, respectively.ConclusionsSurgeons need to be aware of limitations in preoperative predictions of the presence of lymph node metastasis for clinical stage early gastric cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-015-1940-3) contains supplementary material, which is available to authorized users.