Little clinical evidence has been provided to show the minimization of radiation resistance of tumors using high linear energy transfer radiation. We therefore investigated the radiobiological and molecular pathological aspects of carbon beam therapy. A total of 27 patients with squamous cell carcinoma (SCC) of the cervix were treated using a carbon beam and 50 control patients with SCC of the cervix using a photon beam. The expression of Ki-67, p53, and p27 proteins before radiotherapy and 5 and 15 days after therapy initiation were investigated using immunohistochemistry. Similar changes were observed in Ki-67 labeling index (LI) and p53 LI during carbon and photon beam therapies. However, for carbon beam therapy, the mean p27 LI significantly decreased from 25.2% before treatment to 18.6% on the 5th day after treatment initiation, followed by a significant increase to 36.1% on the 15th day. In contrast, for photon beam therapy, the p27 LI consistently decreased from the initial 19.9% to 13.7% on the 15th day. Histological effects were observably stronger under carbon than photon beam therapy, though no statistically significant difference was observed (p = 0.07 on the 5th day and p = 0.10 on the 15th day). The changes in p27 LI under carbon beam therapy were significantly different from those under photon beam therapy, which suggests important molecular differences in the radio-biological response between therapies. Further investigation is required to elucidate the clinical relevance of these putative changes and optimize the relative biological effectiveness of carbon beam to X-ray.