Changes in the quantity and quality of soil organic carbon, and their effect on soil aggregate stability as a result of growing different crops in rotation with wheat, were investigated on a red earth (Oxic Paleustalf) in Wagga Wagga, New South Wales, Australia. After two cycles of the 1:1 rotation, while the total organic carbon in the 0-5cm soil depth was similar (15.1 g/kg), significant differences in water stable aggregation were observed in the order: wheat/lupin = wheat/barley > wheat/canola > wheat/field pea. Using a selective extraction technique, significant differences in the quality (composition) of the soil organic carbon were detected in the soils from the different rotations. Soil from the lupin rotation had the highest salt- and acid-extractable carbon whereas that from the barley rotation had the highest level of hot-water-extractable carbon and microbial biomass carbon. Rather than total carbon or other extractable fractions, the observed differences in aggregate stability were only significantly (P<0.05) related to microbial biomass carbon, which made up only 1.3-1.7% of the total carbon pool. Multiple linear regression analysis indicated that with the exception of salt-extractable carbon, inclusion of any other of the less labile fractions failed to improve the correlation relationship. The labile nature of the microbial biomass carbon therefore accounted for the transient existence of the differences in aggregate stability under different rotation crops. The latter was found to be transient and disappeared at the end of the subsequent wheat crop.