Genetic variation has a profound effect on the nutritional and anti nutritional profile of pulses. Thus, investigating this fact, comparison of five desi and four kabuli varieties of chickpea were done to assess the effect of genetic variation on the anti nutritional factors, bioavailability of minerals and the influence of hydrothermal (autoclaving, microwave cooking, boiling) and dry roasting processing methods. Results showed that large variability exist in antinutritional and mineral content of selected chickpea cultivars. Antinutritional factors (viz. phytate, tannin and trypsin inhibitor’s content) was found significantly (p<0.05) higher in all desi cultivars of chickpea than their kabuli counterparts. All hydrothermal, thermal and bio processing treatments were found to reduce antinutritional factors in all the cultivars of chickpea. Molar ratios of phytic acid with zinc and iron were high in all selected chickpea cultivars which showed poor bioavailability before processing. The bioavailability of iron and zinc were significantly (pd”0.05) improved as a result of all hydrothermal and thermal processing treatments which were applied in this study. Bioavailability of Fe and Zn was higher in case of kabuli cultivars (8.1% and 40.5%, respectively) than desi cultivars (5.5% and 38.4%, respectively). The most pronounced increment among all the processing treatments of in vitro bioavailability of iron and zinc was with autoclaving treatment (17.5 to 30.9% and 25.6 to 41.4%, respectively) followed by microwave cooking, boiling and roasting. Hydrothermal processing treatments particularly autoclaving shows highest reduction in antinutritional factors and improvement in the availability of iron and zinc in all the cultivars of chickpea. Therefore, promotion of suitable cultivars and proper processing treatment should be encouraged.