Owing to its physical properties, particle therapy (PT), including proton beam therapy (PBT) and carbon ion therapy (CIT), can enhance the therapeutic ratio in radiation therapy. The major factor driving PT implementation is the reduction in exit and integral dose compared to photon plans, which is expected to translate to reduced toxicity and improved quality of life. This study extends the findings from a recent systematic review by the current authors which concentrated on tumour outcomes for PT, to now examine toxicity as a separate focus. Together, these reviews provide a comprehensive collation of the evidence relating to PT outcomes in clinical practice. Three major databases were searched by two independent researchers, and evidence quality was classified according to the National Health and Medical Research Council evidence hierarchy. One hundred and seventy-nine studies were included. Most demonstrated acceptable and favourable toxicity results. Comparative evidence reported reduced morbidities and improvement in quality of life in head and neck, paediatrics, sarcomas, adult central nervous system, gastrointestinal, ocular and prostate cancers compared to photon radiotherapy. This suggestion for reduced morbidity must be counterbalanced by the overall low quality of evidence. A concerted effort in the design of appropriate comparative clinical trials is needed which takes into account integration of PT's pace of technological advancements, including evolving delivery techniques, image guidance availability and sophistication of planning algorithms.