Tillage influence soil aggregation, microbial activity in the soil and enhance the oxidation of soil organic carbon (SOC). A long term study was carried out to investigate the impact of conservation tillage on soil aggregates, SOC and microbial biomass carbon (MBC) in rice (Oryza sativa)-wheat (Triticum aestivum) cropping system at experimental station of Varanasi, Uttar Pradesh under the aegis of All India Co-ordinated Research Project (AICRP) of Integrated Farming Systems (IFS) during 2003-10. The four rice crop establishment techniques i.e., direct seeding in zero tilled soil (P-1), wet seeding of sprouted rice seed with drum seeder in puddled condition (P-2), manual transplanting in puddled soil (P-3) and mechanical transplanting in puddled soil (P-4) served as horizontal treatments while four tillage practices in wheat (i.e. T-1- rotavator till drill, T-2- conventional sowing, T-3- strip till drilling, T-4- Zero till drilling) served as vertical treatments in strip plot design with three replications. Total water stable aggregates (WSA)(>0.053 mm) in the soil at surface 0-15 cm depth, ranged between 69.92 and 88.78 % in rice crop, while in winter crop it varied between 74.62 and 83.57 %. According to mean weight diameter (MWD) different treatments in regard to crop establishment technique of rice could be ranked in the order P-1 > P-4> P-2 > P-3 and T-4 > T-3 > T-1 > T-2 in wheat strip regarding tillage practices. However, the MWD decreased drastically in lower soil depth. The SOC ranged from 4.06 to 5.67 g kg(-1) in soil samples from rice plots and from 4.32 to 5.24 g kg(-1) in different tillage treatments in wheat at surface 0-15 cm layer. SOC contents in direct seeding in zero tilled rice strip (5.67 g kg(-1)) and zero till drill in wheat strip (5.24 g kg(-1)) were significantly higher than other treatments in all soil depth. The MBC of direct drilling zero tilled (441 mu g g(-1)) in rice strip and zero till drill in wheat strip (395 mu g g(-1)) had the highest values while the manually transplanted-puddled (383 mu g g(-1)) rice and conventional wheat sowing had the lowest values (334 mu g g(-1)) at all the depths. The differences were significant in at P<0.01 for both SOC and MBC and ranked in order of P-1 > P-2 > P-4 > P-3 of rice crop strip and T-4 > T-3 > T-1 > T-2 in wheat crop strip under 0-15 cm soil depth. The decrease in SOC an average all treatments was about 51 and 89 percent from layer 0-15 to 15-30 and 30-45 cm, respectively. The interaction effects of P at same level of T and T at same level of P treatments on MWD, SOC and MBC were significant (P < 0.01) in 0-15 and 15-30 cm soil depth.