The pathogenesis of L-cystine kidney stones involves four critical steps: nucleation, crystal growth, crystal aggregation, and crystal adhesion to cells. Although inhibition of crystal growth by L-cystine "imposters" at L-cystine crystal surfaces has been suggested as a plausible route for the suppression of stones, understanding the factors that govern crystal-crystal aggregation and adhesion of crystals to epithelial cells also is essential for devising strategies to mitigate L-cystine stone formation. Chemical force microscopy performed with atomic force microscope tips decorated with functional groups commonly found in urinary constituents that likely mediate aggregation and attachment (e.g., COOH, NH2, SH, CH3, OH) revealed signatures that reflect differences in the chemical affinity of these groups for the (001) and {100} faces of the naturally occurring hexagonal form of L-cystine single crystals and the {110} faces of the non-native tetragonal form. These signatures can be explained by the different chemical compositions of the crystal faces, and they reveal a remarkable binding specificity of the thiol group for the sulfur-rich {100} and {110} faces of the hexagonal and tetragonal forms, respectively. Collectively, these observations suggest that alterations of the crystal habit and polymorph by crystal growth inhibitors may not affect crystal aggregation or adhesion to cells significantly.