Abstract Flatulence and fullness of stomach is one of the most common problem associated with chickpea primary due to presence of some oligosaccharides and phenols. In this investigation Desi and Kabuli varieties were compared for these oligosaccharides and phenolic compounds. Furthermore, the effect of different processing and cooking methods such as soaking, cooking and germination in the reduction of these antiphysiological factors were are also studies. Maximum tannic acid (0.90 ± 0.20%) was observed in Parbat and C-44 while minimum (0.60 ± 0.04%) in Karak-2. Stachyose contents ranged between 1.10 ± 0.05 (Karak-3) to 1.42 ± 0.02% (Parbat) while raffinose was 0.63 ± 0.05(Karak-3) to 0.81 ± 0.02% (Dasht). The highest tannic acid content was reduced up to 50% in C-44 by cooking of 72 hours germinated seeds. Stachyose and raffinose contents were completely removed after 72 hours germination. Present studies revealed that cooking after germination is the most effective method to reduce the anti-nutritional factors of chickpea. Individually, soaking and cooking also contributed to the loss of the same factors but to a lesser extent.