Purpose: Radiotherapy causes xerostomia in patients treated for head and neck cancer. This study investigated changes in quality and quantity of saliva after radiotherapy and possible associations between these changes and alterations in oral flora. Materials and Methods: The study was a prospective cohort study of patients receiving radiotherapy for head and neck cancer. Suitable patients were recruited before treatment commenced, and informed consent was obtained. Patients were examined, and provided unstimulated and stimulated saliva samples. Quantity of saliva, buffering capacity and pH were measured. Oral flora was cultured from the saliva samples. Oral clearance of glucose and of lactose was measured. These interventions were repeated at intervals after radiotherapy had been completed. Results: Eighteen patients were recruited. Stimulated and unstimulated saliva flow rates, glucose clearance, salivary pH and buffering capacity were significantly reduced after radiotherapy. Candida albicans counts were significantly increased. These increases were significantly correlated with reductions in stimulated and unstimulated salivary flow rates. Counts of lactobacilli, Streptococcus mutans and Bifidobacteriaceae increased, but not statistically significantly. Conclusions: Therapeutic radiotherapy significantly reduced the quality and quantity of saliva in head and neck cancer patients. These reductions were associated with increased C. albicans counts. Keywords: cancer microflora, quality of life, radiotherapy, saliva, xerostomia