Burning mouth syndrome (BMS) is a multifactorial condition which is still poorly understood. The aim of this study was to evaluate a group of patients with BMS, as compared to a control group, and to describe related local and systemic factors. Records of patients referred to the Oral Pathology Service at the School of Dentistry over a period of 7 years were considered for the study, within which 32 patients with a diagnosis of BMS were found. A randomized group matched for age and gender was also evaluated for the study. Data were analyzed statistically using the SPSS 12.0 for Windows. Prevalence of BMS was 0.99% (32 BMS patients/3,243 records), considering that females were more commonly affected than were males and that the majority of the individuals were in their sixties. The univariate analysis performed comparing the two groups revealed statistical differences concerning the presence of gastrointestinal diseases (p = 0.003) and urogenital diseases (p = 0.012). The intake of H-2 receptor antagonist and proton pump inhibitor drugs (p = 0.015) also proved to be significant. Logistic regression analysis confirmed that gastrointestinal and urogenital problems were indeed risk factors that were solely associated with BMS. Although a diversity of related factors could be identified, gastrointestinal problems were the most prevalent, suggesting that the management of BMS patients requires attention and an appropriate approach to such disorders.