Oral mucositis is a painful condition that occurs in patients who have undergone haematopoietic stem-cell transplantation (HSCT) and has a huge impact on their quality of life. The objective of this study was to examine the extent to which interleukin-6 (IL-6) and tumour necrosis factor alpha (TNF-α) are associated with oral health quality of life among patients who underwent HSCT. A. C. Camargo Cancer Center patients were evaluated over 20 months at 4 different time-points: a) at patient admission (M1); b) on the day of infusion of HSC (M2); c) 12 and 20 days after the first day of the conditioning regimen for autologous and allogeneic transplantation, respectively (M3); and d) 30 days after the first day of the conditioning regimen (M4). Mucositis clinical evaluations were performed using World Health Organization (WHO) criteria. Oral health quality of life was measured using the Oral Health Impact Profile short form (OHIP-14), Oral Mucositis Quality of Life (OMQoL) and Patient-Reported Oral Mucositis Symptom (PROMS) scales. Correlations between clinical data and quality of life scores were examined. STATA 11.0 was used to perform the statistical analyses (5% level of significance). Eighty-two patients participated in the study; 62.2% were male, 28.05% had multiple myeloma, and the mean age was 48.49 years (SD 13.76). Higher scores (worse quality of life) were observed as mucositis scores increased, but the results were not significant. The OMQoL had a high correlation with OHIP-14 (0.8377), but the correlation between the PROMS scale and the OHIP-14 was lower (0.6643). Higher concentrations of IL-6 and TNF-α were associated with worse quality of life, according to all indices (p < 0.05). Oral mucositis was associated with quality of life scores (p < 0.01).