The first step in urinary stone formation is the nucleation of urinary mineral from supersaturated urine. The formed nuclei then grow or/and aggregate to a pathological size. Thus, the nanocrystallites in urine may be related to the formation of urinary stones. Nanocrystallites with a size of less than 1000 nm in the urine samples of 85 healthy persons and 65 lithogenic patients were comparatively investigated using laser scattering spectroscopy, TEM, and X-ray diffraction. Most of the nanocrystallites in healthy urine samples were spheroidal, less aggregated, well-dispersed, and with a narrow particle size distribution from about 20 to 350 nm. In contrast, most of the particles in lithogenic urines had sharply angled edges and tips, were aggregated, and had a broad particle size distribution from 1.1 to 1000 nm. More calcium oxalate dihydrate (COD) nanocrystallites were found in healthy urine; however, more calcium oxalate monohydrate (COM) nanocrystallites were found in lithogenic urine. The morphology, particle size, aggregation, and crystal phase of nanocrystallites in the urine of lithogenic patients are pronouncedly different from those of healthy persons. The results suggest, in ascending order of importance, that making nanocrystallites rounded, diminishing their size differentiation, and decreasing their aggregation in urine by physical and chemical methods maybe the means to prevent urinary stone formation. The most crucial among the four differences is the crystal phase differential of calcium oxalate (CaOxa). That is, the formation of COD nanocrystallites in urine can be considered as being relatively more favorable in preventing stone formation than the formation of COM nanocrystallites, which are in accord with those found for larger crystallites.