Kidney stones are a common form of nephrolithiasis, affecting up to 15% of the world’s population with a high probability of recurrence. These stones exhibit various chemical compositions and crystalline forms associated with different etiologies. Classification of the stones’ components is necessary to optimize treatment and suggest lifestyle changes to reduce the risk of recurrence. Current characterization methods usually require extensive sample preparation or are too detailed for the needs of a high-throughput laboratory. In this article, we present a kidney stone component classification scheme based on the multiphoton response of crushed samples that is label-free, requires minimal sample amounts, and simple preparation. We measure two-photon excited fluorescence, which is sensitive to protein content, second-harmonic generation, which is sensitive to crystalline symmetry, and polarization-resolved third-harmonic generation (pTHG), which is sensitive to crystal heterogeneity and birefringence. The combination of these three contrast modes can distinguish different materials, specifically calcium oxalate in monohydrate (COM), dihydrate (COD), or amorphous forms, cystine, and carbonate apatite. In addition, pTHG images have the potential to distinguish between COM and COD fragments and to provide information on the submicron organization of carbonate apatite fragments.