In this study, clinical, biochemical and histological analysis were used to compare different phototherapies, including LED, low and high-power laser (HPL) for the treatment of chemotherapy (CT)-induced oral mucositis (OM). One-hundred-fifty hamsters were divided into five groups: C: control; CH: CT/OM induction; L: CT/OM induction and treatment with LED (635 nm, 1.2 J), HL: CT/OM induction and treatment with HPL (808 nm, 10 J), LL: CT/OM induction and treatment with low-level laser therapy (LLLT) (660 nm, 1.2 J). OM was induced by scratches performed on check pouch mucosa after two injections of 5-Fluorouracil. The experiment lasted 10 days and OM was analyzed by specific clinical scales on days 5, 7 and 10. The animals were euthanized and the cheek pouch mucosa removed for biochemical (TNF-α concentration) and histological (light microscopy) analysis. After statistical analysis, the authors' results showed LED and LLLT therapies were efficient treatments for OM, decreasing TNF-α concentration on day 7 (p < 0.05) and completely healing the mucosa on day 10. HPL showed no interference in final healing of OM. According to the methodology used and the results obtained in the present study, LLLT and LED therapies were the best choices to decrease the severity of OM, accelerating tissue repair and decreasing the inflammatory process. Clinical evaluation of OM in Groups CH, LL, L and HL and their respective arrangement of phototherapy treatments at different time intervals (5, 7 and 10 days).