Optical Coherence Tomography (OCT) has been used to produce longitudinal images of dental tissues. We investigated the influence on OCT system, of factors that could limit detection and quantitative monitoring of incipient caries. The effect of such factors as saliva, dental plaque, lesion staining, ambient lighting, and Dacron gauze (used to encourage plaque growth in in situ caries studies) on OCT imaging and analysis were determined during demineralization to produce early caries. The system can collect A-scans, B- scans (longitudinal images) and C-scans (en-face images). Caries lesions were shown as volumes of reduced reflectivity. A-scan, which showed the levels of reflectivity versus the depth of penetration into the tooth tissue, was used for the quantitative analysis of the reflectivity loss. The reflectivity of the tooth tissue decreased with demineralization. The percentage change in reflectivity of the tissue was quantified as a measure of the change in mineral status of the tissue following demineralization. Neither the presence of saliva, plaque, Dacron gauze, plaque/Dacron gauze, nor lesion staining nor the level of ambient lighting significantly affected OCT detection and analysis of an incipient caries.