We compared the performance of three widely used linear multivariate methods for autofluorescence spectroscopic tissues differentiation. Principal component analysis (PCA), partial least squares (PLS), and multivariate linear regression (MVLR) were compared for differentiating at normal, tubular adenoma/epithelial dysplasia and cancer in colorectal and oral tissues. The methods' performances were evaluated by cross-validation analysis. The group-averaged predictive diagnostic accuracies were 85% (PCA), 90% (PLS), and 89% (MVLR) for colorectal tissues; 89% (PCA), 90% (PLS), and 90% (MVLR) for oral tissues. This study found that both PLS and MVLR achieved higher diagnostic results than did PCA.