Individuals with oral squamous cell carcinomas (SCCs) have a generally poor prognosis mainly due to late diagnosis of the disease. The identification of early stages of the disease (oral premalignant lesions, OPLs) is crucial to improving outcome. At present, prediction of outcome for OPLs relies on the histological assessment of biopsies for the presence and degree of dysplasia. Unfortunately, pathology is a poor predictor of outcome for the earliest, and most frequently observed OPLs. Our recent study has shown that high-risk OPLs can be identified by assessing for loss of heterozygosity (LOH) using microsatellite analysis. Unfortunately, both molecular and histological assessments depend on the availability and accuracy of a biopsy. The determination of when and where to biopsy OPLs is a continuing challenge facing clinicians. In experienced hands, toluidine blue (TB) staining can be used to facilitate such determinations. However, at present it is not clear whether TB-positive OPLs differ in molecular alterations and cancer risk from negative lesions. The objective of this thesis was to determine whether LOH profiles were different in TB positive and negative OPLs. A total of 67 OPLs were evaluated for TB staining, and assessed for LOH using 11 microsatellite markers on chromosome arms: 3p, 9p, and 17p. The main finding of the thesis was that TB-positive cases had a high-risk LOH than negative cases. They showed increased losses on multiple regions (P = 0.004), at 3p (P = 0.04), 9p (P =0.007), and 17p (P = 0.0001). This positive association between TB staining and LOH was independent of dysplasia. TB positive cases of hyperplasia or low-grade dysplasia showed higher frequencies of LOH at any loss (P = 0.006) and at 17p (P = 0.005). In conclusion, these data show that patterns of allelic loss are different in TB-positive and TB-negative lesions with an increased proportion of cases showing patterns with an elevated risk of progression. The data support the use of this dye by clinicians to identify tissue that requires biopsy.