Although crystalluria is generally considered a normal finding, sometimes it gives evidence of renal disturbance. Thus, detection and identification of urinary crystals may provide useful data for understanding the etiology of mechanism of the disorder. Light microscopy may be not sufficient to accurately identify the crystals. We investigated the ability of Fourier transform infrared microscopy (FTIRM) to identify isolated crystals of clinical interest. Twenty-five urine samples presenting crystalluria were tested because of their unusual aspect. We successfully identified 16 compounds and showed that crystals with the same apparent morphology can be composed of different substances. Moreover, an unexpected structure may be an insoluble phase of a drug metabolite. We conclude that FTIRM is a good technique for investigating urinary crystals of clinical interest.