The functional properties of native and modified starches are affected by other food components such as organic acids. The objective of this study was to determine the effects of citric and malic acids as two common organic acids in foods on some properties of native and cross-linked wheat starches. Acids (150mg/kg starch basis) were added to a starch suspension (40%w/w) and held for 30min at 25 degrees C, neutralized, washed, dried, and sieved. Scanning electron microscopy showed that both acids caused some spots on the surface of the granules. The acids reduced intrinsic viscosity and water absorption, while increased water solubility of the samples. Determination of the thermal properties showed that malic acid significantly reduced the gelatinization temperature and enthalpy of gelatinization while citric acid had no significant effect on these parameters. Both acids decreased hardness, adhesiveness, elasticity, and cohesiveness of the starch gels. In general, malic acid was more effective than citric acid on the functional properties of both starches. Native wheat starch was more sensitive to these acids than the cross-linked starches.