Treatment-related toxicity is common in the radiotherapeutic management of cancers of the gastrointestinal tract. These toxicities can diminish treatment efficacy by necessitating treatment breaks, limiting the radiation dose that can be delivered, and hindering concomitant use of chemotherapy and targeted drug agents. Many efforts have focused on widening the gap between the likelihood of tumor control and the likelihood of toxicities associated with radiation. Use of particles that exhibit a Bragg peak phenomenon in their interactions with tissue, such as protons, heavier ions like carbon ions, and pions, is one means of concentrating radiation dose in tumors and away from normal tissues. Neutron beams have also been used in the treatment of gastrointestinal cancers in an effort to take advantage of their potent biologic effects. This report reviews basic particle radiation physics and biology, as well as the clinical experience with protons, heavier ions, pions, and neutrons in the treatment of various gastrointestinal malignancies. Potential future directions in clinical research with particle therapy are discussed.