The thermal behavior of discrete phases formed in the respective systems of malic acid enantiomers and L-enantiomers of the amino acids valine and isoleucine was studied using the temperature-resolved PXRD method. In the (S)-malic acid–(R)-malic acid system, thermal deformations in crystal structures of stable compounds (enantiomer S, racemates RSI and RSII, and non-equimolar compound S₃R) and polymorph transformations of metastable compounds (racemate RSIII and non-equimolar compound 3S1R) were examined. In the L-valine–L-isoleucine system, thermal deformations in crystal structures of stable compounds L-Val and L-Ile and non-equimolar compound V₂I were investigated. Thermal deformation analysis included plotting the temperature dependence of the unit cell parameters and volume, calculating thermal deformation tensors, plotting figures of thermal expansion coefficients (CTE), and estimating the extent of thermal deformation anisotropy. In all the cases studied, the maximal thermal expansion was observed in the direction of the weakest hydrogen (malic acid) or van der Waals (valine and isoleucine) intermolecular bonds, i.e. in the directions closest to that perpendicular to the dimer molecule chains (malic acid) or to molecular layers (valine and isoleucine). The strongest anisotropy of thermal deformations in monoclinic crystals was observed in the ac plane, in which the symmetrically unfixed angle β can vary.