Dentin morphology and the lesion found in dental caries have been studied for many years. It was first observed under optical microscopy, and later using electron microscopy. Confocal laser scanning microscopy (CLSM) applied with several fluorescent dyes such as alizarin red to see normal dentinal tubules. However, as far as authors aware, the CLSM studies of dentinal tubules in human caries using alizarin red is rare. The aim of this study is to examine histopathological and morphological changes in dentinal tubules of dentin caries stained with alizarin red using CLSM. Fifteen extracted carious teeth (premolar or molar) was collected and fixed in neutral formalin solution buffered with phosphate buffer, rinsed and stored in calcium free phosphate buffer saline (PBS) at 4°C. The specimens were dehydrated and embedded in resin. Longitudinal or cross sections were cut and polished and then stained with alizarin red S (100 μg/ml) in 0.5 M HCl solution for 24-48 hour at 37°C. After dehydration specimens were mounted on glass slide and examined under CLSM using epi-flourescent mode or transmission light mode with wave length of 512 nm. The images of dentinal tubules were taken serially and optimum images of three-dimensional structures were reconstructed using software of CLSM. Histopathological changes of dentinal tubules in human caries showed area of demineralized dentin, translucent zone, and normal area. The dentinal tubules were thin and had numerous branches. In conclusion, confocal microscopy revealed Study shows that confocal microscopy revealed histopathological changes in dentinal tubules affected by carious lesions.