IR spectroscopy and principal components analysis (PCA) of endocervical cells and smears diagnosed with benign cellular changes were investigated to determine the influence of these potential confounding variables in the diagnosis of cervical cancer. Spectral differences in all cell and diagnostic types investigated were found in the phosphodiester and carbohydrate regions. However, the spectral differences in other bands were not distinct enough to allow differentiation between groups. The PCA was successfully used to obtain a separation of normal ectocervical smears from normal endocervical cells and smears diagnosed with inflammation, Candida albicans, and bacterial vaginosis. A separation with a slight overlap of abnormal ectocervical smears from normal endocervical cells, inflammation, and bacterial vaginosis was obtained with PCA. Candida was not separated from abnormal ectocervical smears with any success.