To compare the survival outcomes of transabdominal (TA) and transthoracic (TT) surgical approaches in patients with Siewert-II/III esophagogastric junction adenocarcinoma. This retrospective study was conducted in patients with Siewert-II/III esophagogastric junction adenocarcinoma who underwent either TT or TA operations in the West China Hospital between January 2006 and December 2009. A total of 308 patients (109 in the TT and 199 in the TA groups) were included in this study with a follow-up rate of 87.3%. The median (P25, P75) number of harvested perigastric lymph nodes was 8 (5, 10) in the TT group and 23 (16, 34) in the TA group (P<0.001), and the number of positive perigastric lymph nodes was 2 (0, 5) in the TT group and 3 (1, 8) in the TA group (P<0.004). The 5-year overall survival (OS) rate was 36% in the TT group and 51% in the TA group (P=0.005). Subgroup analysis by Siewert classification showed that 5-year OS rates for patients with Siewert II tumors were 38% and 48% in TT and TA groups, respectively (P=0.134), whereas the 5-year OS rate for patients with Siewert III tumors was significantly lower in the TT group than that in the TA group (33% vs. 53%; P=0.010). Multivariate analysis indicated that N2 and N3 stages, R1/R2 resection and a TT surgical approach were prognostic factors for poor OS. Improved perigastric lymph node dissection may be the main reason for better survival outcomes observed with a TA gastrectomy approach than with TT gastrectomy for Siewert III tumor patients.