Background: Prognostic factor in patients with HER2 positive gastric cancer who received trastuzumab (T-mab) based chemotherapy remains unclear. The aim of this study is to reveal the clinical factors which predict prognosis in T-mab based chemotherapy. Methods: We retrospectively reviewed HER2 positive gastric cancer patients treated with T-mab based chemotherapy in our institute from March 2011 to June 2016. Patients’ demographics according to the ToGA study and laboratory data were examined. Results: Total of 143 patients were enrolled. Median follow-up period was 14.9 months, and median progression-free survival (PFS) and overall survival (OS) were 11.2 months (95% CI: 8.6-13.9) and 20.9 months (95% CI: 16.6-25.2), respectively. In univariate analysis, performance status (0 vs. 1-2), present of measurable lesion, presence of visceral metastases, No. of metastatic lesion (1-4 vs. > 4), LDH, ALP, Alb, median CEA (≧ 13.6 mg/ml vs. < 13.6mg/ml), and median Neutrophil/Lymphocyte (N/L) ratio (≧ 3.11 vs. < 3.11) were significantly associated with PFS. Regarding OS, extension of disease (locally advanced vs. metastatic), presence of visceral metastases, No. of metastatic lesions, Hb, ALP, Alb, CRP, median CEA and median N/L ratio were significant. In multivariate analysis, CEA levels (HR 0.54: 95%CI 0.34-0.86, p = 0.010) and ALP (HR 0.57: 95%CI 0.33-0.99, p = 0.046) retained to be significant in regard to PFS. Patients with < median CEA level had a median PFS of 13.1 months vs. 7.2 months with ≧ median CEA level. Patients with normal level of ALP showed a median PFS of 12.8 months vs. 5.9 months with abnormal ALP level. With respect to OS, CEA levels (HR 0.59: 95%CI 0.34-1.03, p = 0.061) and N/L ratio (HR 0.55: 95%CI 0.29-1.06, p = 0.074) were marginally significant. Patients with < median CEA level had a median OS of 27.6 months vs. 17.6 months with ≧ median CEA level. Patients with > median N/L had a median OS of 24.5 months vs. 16.5 month with ≧ median N/L. Conclusions: Lower CEA levels and normal ALP levels were associated with favorable PFS, and lower CEA and N/L ratio were marginally associated with favorable OS.