As a basis for crystallization studies, the solubilization of amino acids (glycine, l-histidine, and L-phenylalanine) in water-in-isooctane microemulsions stabilized by AOT (sodium di-2-ethylhexyl sulfosuccinate) was investigated. The maximum amount of amino acid that could be solubilized was determined by the solid-liquid extraction method, and the effect of the guest molecules (amino acids) on the size and shape of the microemulsion droplets and their thermal properties were determined using SAXS and DSC measurements, respectively. The solubilization of glycine molecules, which primarily dissolve in the water pool, was slightly lower than their solubility in pure water, decreasing with increasing concentration of AOT and increasing with increasing water content in the microemulsion. In contrast, the solubilization of phenylalanine, which is primarily located at the water/oil interface, exceeded several times the solubility in water, the solubilized amount increasing with increasing AOT and/or water concentrations. Histidine had characteristics intermediate between these two extremes. Solubilization of those molecules effected an increase in droplet size. The thermal analysis showed that loading of the microemulsion droplets with glycine has a much stronger effect on the thermal behavior of the emulsified water than has loading with phenylalanine. The low solubilization of glycine as compared to its solubility in pure water can be explained by the state of water within the microemulsion droplets, i.e., part of it is present as free water and part as water bound to the AOT headgroups. The loading of phenylalanine changed the shape of the microemulsion droplets from spherical to ellipsoidal, and with increasing droplet sizes, the [phenylalanine]/[AOT] molar ratio at the interface increased.