In the present study sunflower protein isolates were subjected to heat treatment (80 °C for 5 min, 15 min and 25 min) at three pH values (3.5, 4.5 and 5.5). The strength of gel prepared from treated protein isolates was lower than the gels from native protein isolates and gel strength increased with increase in temperature treatment. Higher denaturation temperatures were observed in treated protein isolates than native protein isolates and increased with increase in thermal treatment time. Treated protein isolates showed more resistance against thermal degradation than native protein isolates as was evident from thermal gravimetric analysis. Secondary and tertiary structure determined by circular dichroism and intrinsic fluorescence respectively were significantly altered after thermal treatment. Lower crystal size along with reduced crystallinity was observed in treated protein isolates than native protein isolates and was further reduced with increase in heating time as was determined by X-ray diffraction.