Chemoradiotherapy for Locally Advanced Head and Neck Cancer (LAHNC) has varied immensely in the last 20 years with the evolution of conformal Radiotherapy techniques. Whether differences exist in these treatment techniques related to survival and toxicity, remains unanswered. Also, these vulnerable groups of subjects have an enhanced risk of oral Candidiasis, mainly because of immune suppression and mucosal damage. A two-year cross-sectional pilot study was conducted in Barpeta Cancer Centre, Barpeta District, Assam. Two hundred cases with histological confirmation of LAHNC under definitive chemoradiotherapy treatment of 66-70 Gy were included. Sequential boost (SB) was used to treat 130 patients and Simultaneous Integrated Boost (SIB) was used upon 70 patients as separate treatment arms. In both treatment arms Inj. Cisplatin 40 mg/m2 per week was included as a simultaneous chemotherapeutic. Grading of toxicity was done every week after treatment initiation and during follow-up visits at the end of three (3) months post treatment. Overall survival (OS), Recurrence free survival (RFS) and Disease free survival (DFS) were estimated. Saliva samples were collected from each patient during the first follow up and inoculated on SDA with chloramphenicol. Germ tube test, Dalmau plate culture and Chrom Agar inoculation was used for speciation. The most common subtype was oropharyngeal carcinoma with no treatment-related death in either arm. The OS was estimated to be 70% in SB arm and 62% in the SIB treatment Arm, at the end of 2 years. SIB Arm showed high rates of advanced grade toxicities then SB Arm. Oral candidiasis prevalence was 65%, but was higher in SIB (71.4%) then SB arm (61.5%), and Candida albicans (46%) largely outnumbered candida Non-albicans. Significant association was found between high grade mucositis (χ2 = 17.45, P < 0.001), dysphagia (χ2 = 28.79, P < 0.001), dermatitis (χ2 = 42.23, P < 0.001) with Candidal growth. Disease related outcomes showed no changes in both the treating arms. However toxicities and Candidal growth especially Candida albicans showed high association, warranting early interventions with oral care and antifungal therapies.