Radiotherapy has been recognized as a valuable modality of treatment in the management of head and neck cancers. It can have a direct bactericidal effect on the normal flora of the oropharynx. The objective of this study is to determine the changes in the oropharyngeal flora after external beam radiation. This prospective non randomized control study was performed to aid in identification of organisms involved in sepsis, as well as aid in choosing appropriate antibiotics for surgical procedures in irradiated patient. Forty patients with various head and neck malignancy and thirty control patients were selected. Oropharyngeal swabs were taken prior to radiotherapy, at the end and one month after radiotherapy. A single swab was taken from the control group. A full bacteriological analysis was performed. There was a statistically significant decrease in Alpha Hemolytic Streptococci and Neisseria species post radiotherapy. B Proteus and Candida Albicans showed a statistical significant increase in patients with head and neck cancer post radiotherapy. These changes remained even one month after radiotherapy.