Thermal alkaline treatment, normally used for corn, was applied to pigeonpea grains. Starch granules were isolated using wet milling and alkaline treatments. Effects of the calcium hydroxide [Ca(OH)(2)] concentration in the range of 0-1% (w/v) on granule structure, crystalline structure, chemical composition, and physicochemical, thermal, and pasting properties of isolated starch granules were determined. Compared to native samples, thermal alkaline treated samples had higher protein, lipid, calcium, and phosphorus contents, but lower starch and amylose contents. Thermal alkaline treatment increased starch granular size and gelatinization temperatures, but decreased relative crystallinity, gelatinization enthalpy, swelling power, solubility, amylose leaching, and the pasting viscosity. Amylose-lipid complexes were not found in thermal alkaline treated flours. As the Ca(OH)(2) concentration increased, the amylose content, relative crystallinity, gelatinization temperature, and enthalpy also increased, but the swelling power, solubility, amylose leaching, and paste viscosity decreased. A higher Ca(OH)(2) concentration produced more stable starch granules that resisted re-gelatinization.