Carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) are important biogenic green house gases (GHGSs) from agricultural sector contributing to global warming. Temperature and rainfall play an important role in GHGS fluxes and information on their role in rainfed crops and systems is very scanty. Field studies were conducted at Hyderabad, India during 2012 rainy season to quantify GHGSs fluxes from two important food crops grown widely in rainfed regions viz. sorghum and pigeonpea. Quantum of fluxes ranged from 26 - 85 mg CO2 - C m-2 h-1 in case of CO2 and 18 – 68 μg N2O-N m-2 h-1 in case of N2O at different stages of crop growth. Cumulative seasonal fluxes are 1.18 and 1.24 Mg CO2-C ha-1 and 0.78 and 0.94 kg N2O-N ha-1, in sorghum and pigeonpea, respectively. Ambient temperature and rainfall significantly influenced CO2 fluxes. CO2 fluxes increased with increase in temperature from 25.9 °C to 31 °C and fluxes were highest at 28.4 °C in pigeonpea and at 27.7 °C in sorghum. Quantum of CO2 fluxes were highest at grain filling stage in sorghum and grand growth period in pigeonpea. N2O fluxes increased with increase in temperature and moisture availability. These results provide evidence that rainfed crops in semi-arid regions contribute significant CO2 and N2O fluxes which are influenced by temperature and rainfall, thus warrant further studies.