Gastritis cystica profunda (GCP) is a rare disease that shows multiple cystic gastric glands dispersed within the submucosa of the stomach. GCP occurs most commonly in patients who have undergone previous gastric surgery and presents as subepithelial tumor or a polypoid lesion. Here, we report the case of GCP in a 79-year-old patient who had undergone Billroth II gastric resection. During upper gastrointestinal endoscopy multiple lesions like tiny holes in the mucosa were observed. Endoscopic ultrasound showed cystic structures in the gastric submucosa. Biopsies finally proved the dispersed mucosal glands in the submucosa, which are pathognomonic for GCP. So far, in all published cases, GCP presented as polypoid lesions with no mucosal damage in upper gastrointestinal endoscopy. It is for the first time that GCP has been diagnosed with cystic lesions connected to the gastric lumen with a porus in each of the cysts.