The aim of this study was to follow the long-term effects of radiation therapy of head and neck malignancies on oral yeast colonization, mucositis and salivary function. Included in this prospective study were 32 patients with intended radiation therapy of a malignancy of the head and neck. In all patients the salivary glands lay within the radiation field and the patients had at least five teeth. The first examination was performed after oral hygiene instruction and removal of questionable teeth before the start of radiotherapy. The following examinations were conducted after 3, 6, 9 and 12 months. Together with the quantitative determination of Candida colonization, three "mucositis" variables were assessed: (1) examiner-rated mucositis score (LENT/SOMA), (2) patient-rated mucositis symptoms, and (3) scintigraphic salivary excretion fraction. The maximum Candida colonization was found 6 months after radiation therapy and this declined to above normal values after 12 months. Salivary flow was at a minimum 6 months after radiation therapy and had slightly recovered by 12 months. Examiner-rated mucositis and patient-rated xerostomia showed no significant recovery after 6 or 12 months. The results of this study show slight recovery of the oral ecological system. Although the causal role of a single parameter is not clear, persistently elevated Candida colonization should be taken into account therapeutically.