Radiation therapy plays an important role in the management of malignant tumors, however, the problem of radiation resistance resulting in tumor recurrences after treatment is still unsolved. The emergence of novel biomarkers to predict cancer cell insensitivity to ionizing radiation could help to improve therapy results in cancer patients receiving radiation therapy. The proteomic approach could be effectively used to identify proteins associated with cancer radiation resistance. It is generally believed that radiation resistance could be associated with cancer stem cell persistence within the tumor. Therefore, determination of the molecular characteristics of cancer stem cells could provide additional possibilities to discover novel biomarkers to predict radiation resistance in cancer patients. This review addresses proteome-based findings that could be used for further biomarker identification and preclinical and clinical validation.