The relationship between the serum pepsinogen (sPG) level and changes in gastric mucosa has been well studied. Here, we evaluated the usefulness of sPG (I, II, I/II ratio) and intragastric pH as a biomarker of severe gastric atrophy in gastric neoplastic lesions. A total of 186 consecutive Korean patients with gastric neoplastic lesions underwent endoscopic submucosal dissection (ESD) in this study. The serologic atrophy group had sPG I level ≤ 70 ng/mL and an sPG I/II ratio ≤ 3.0. Before ESD, overnight fasting venous blood and gastric juice samples were collected to measure the sPG level and intragastric pH. The degree of gastric atrophy was estimated by endoscopy, and the rapid urease test was performed to investigate Helicobacter pylori infection. Patients who met the criteria of serologic atrophy showed more severe endoscopic atrophic changes (61% vs. 18%, p = 0.000). Older patients and those with more atrophic changes at the gastric upper body demonstrated both a lower sPG I level and a lower PG I/II ratio and more severe endoscopic atrophy. The sPG I/II ratio was the lowest in low grade dysplasia than in high grade dysplasia and early gastric cancer (EGC) (p = 0.015). In addition, patients who tested negative for serologic atrophy and H. pylori showed the lowest intragastric pH (p = 0.000). A low sPG I level and a low I/II ratio were correlated with the severity of gastric atrophy in gastric neoplastic lesions, thus indicating it to be a sensitive biomarker of gastric precancerous lesions or EGC.