Background: Radiotherapy for head and neck cancers (HNC) causes alteration of oral mucosal barrier predisposing it to colonization and infection. Such infections often result in pain and burning sensation thus contributing to major morbidity. Objective: 1. To identify the fungi isolated from the patients undergoing radiotherapy for HNC. 2. To determine their antifungal susceptibility and week of colonization. 3. To find out association between oral fungal infection and severity of oral mucositis. Materials and methods: Study was done on 50 patients of HNC treated with concurrent chemoradiotherapy. Three samples (throat, urine, blood) were collected for fungal culture and sensitivity. These samples were collected before the start of radiotherapy, during radiotherapy (2nd and 6th week) and post radiotherapy (10th week). Results: Only 49 patients were available for analysis. Fungal infection was found in 27/49 patients (55.10%) out of which Non-albicans Candida was isolated in 18/49 (36.73%) and Candida albicans in 9/49 (18.36%) cases. About 66.66% (18/27) isolates were sensitive to fluconazole. Maximum isolation of yeast was during 6th week of radiotherapy. All grade 4 and 71.42% of grade 3 oral mucositis were found in patients who were positive for fungal infection. Conclusion: The spectrum of fungal species in throat swab was: Non-albicans Candida and Candida albicans observed in 36.73% and 18.36% of patients respectively. Higher rate of fungal colonization and infection was found in patients with grade 3/4 oral mucositis. Prophylactic fluconazole in HNC patients on concurrent chemoradiotherapy has the potential to reduce emerging invasive fungal infection and its associated morbidity. (C) 2017 National Cancer Institute, Cairo University. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license.