Abstract Background Syphilis is a sexually transmitted infection caused by Treponema pallidum and can clinically progress through four different stages. Syphilitic gastritis is one of the rare manifestations of the disease, harboring the potential to mimic several types of unrelated disorders such as malignant lymphomas, Langerhans cell histiocytosis, auto-immune gastritis and refractory Helicobacter pylori infection. The classics symptoms are weight loss, abdominal pain, and gastroparesis, nausea, vomiting and hematemesis. The most common endoscopic finding is gastric ulcers. The rising trends of syphilis in the last decade, detected in both developing and developed countries, calls for continued efforts for case detection on rare syphilis manifestations. Methods A 35-year-old male patient was submitted to gastric biopsy due to endoscopic findings of multiple polyps in the corpus and antrum of stomach. The material was processed and analyzed in a pathology laboratory in São Paulo, Brazil. Histological sections were stained with hematoxylin and eosin and immunohistochemical staining. Results The specimens exhibited intense inflammatory lympho-histiocytic infiltrate, rich in plasma cells, neutrophils and eosinophils affecting the gastric mucosa. Immunohistochemical staining revealed spiral-shaped bacteria consistent with T. pallidum affecting the gastric mucosa surface, adjacent to vessels, and permeating glands. Conclusions This case report has the goal of showing the occurrence of syphilitic gastritis, an uncommon extracutaneous manifestation of T. pallidum infection with the potential to mimic other etiologies. Due to the rarity of syphilitic gastritis and its non-specific symptoms, a combination of clinical, endoscopic, and histopathological findings is necessary to secure diagnosis of syphilitic gastritis. The advent of immunohistochemistry for T. pallidum has facilitated microscopic diagnosis, as special stains such as Warthin-Starry can still pose interpretation challenges.