Background: Radiotherapy of gastric mucosa-associated lymphoid tissue (MALT) lymphoma should be delivered to the whole stomach with optimal planning target volume (PTV) margins that account for variations in stomach volume, respiratory movement, and patient set-up error. In this study, we evaluated whether the use of four-dimensional cone-beam computed tomography (4D-CBCT) reduces the PTV margin.Methods: Eight patients underwent radiotherapy with 15 fractions of gastric MALT lymphoma using 4D-CBCT. Structures with PTV margins of 5–30 mm (5 mm intervals) from the internal target volume of the stomach defined based on the 4D-CT images were generated. For the target localization, we performed matching based on skin marking (skin matching), bone anatomy (bone matching), and stomach anatomy (4D soft-tissue matching) based on registration between planning CT and 4D-CBCT images from 10 phases. For each patient, we calculated the covering ratio (CR) of the stomach with variable PTV margins, based on the 4D-CBCT images, with a total of 150 phases [CR (%) = (number of covering phases / 150 phases) × 100], for three target localization methods. We compared the CR values of the different target localization methods and defined a minimal PTV margin with an average CR of ≥ 95 % for all patients as optimal.Results: The average CR for all patients increased from 17.9 % to 100 %, 19.6 % to 99.8 %, and 33.8 % to 100 %, in the skin, bone, and 4D soft-tissue matchings, respectively, as the PTV margins increased from 5 to 30 mm. The CR obtained by 4D soft-tissue matching was superior to that obtained by skin (P = 0.013) and bone matching (P = 0.008) for a PTV margin of 15 mm. The optimal PTV margins were 20 mm (average CR: 95.2 %), 25 mm (average CR: 99.1 %), and 15 mm (average CR: 98.0 %) for the skin, bone, and 4D soft-tissue matchings, respectively.Conclusions: This study demonstrates that the use of 4D-CBCT reduces the PTV margin when applying 4D soft-tissue matching, compared to skin and bone matchings. Additionally, bone matching does not reduce the PTV margin as compared with traditional skin matching.