Because cholesterol crystals (Chcs) are a major cause of atherosclerosis, imaging Chcs in tissues with high sensitivity and specificity is important in diagnosing and predicting atherosclerosis. Polarizing microscopy (PM) has been widely used to image crystalline materials in tissues, but it has been difficult to distinguish Chcs from other crystalline materials in tissues. Thus, various methods such as fluorescent dye staining, Raman spectroscopy, and two-photon microscopy (TPM) have been developed to image Chcs with high sensitivity and specificity. However, these methods require expensive equipment or complex processes. Therefore, we have developed a low-cost, easy-to-use PM system using an LED light source that can distinguish Chcs from other crystalline materials with high sensitivity and specificity. Due to the nature of the LED spectrum in our system, collagen is displayed in yellow and Chcs in blue. In addition, we have improved the sensitivity and specificity by creating an aqueous condition on the sample. In the aqueous state, signals of yellowish collagen fibers were reduced and signals of Chcs were highlighted. The Chcs detection capability of our system was verified compared with the TPM image. In addition, clinical feasibility was shown by comparison with existing histological methods.