The extent to which land management practices are sustainable depends on the maintenance of soil quality from the physical, chemical and biological perspectives. However, there is little information on soil quality in Mediterranean environments where climatic factors limit carbon (C) input and yet promote mineralization of what little C is returned to the soil. The impact of any soil and crop management practice on soil quality attributes in any ecosystem can only be objectively assessed under long-term agronomic trials. In such trials, especially in fragile, semi-arid regions, little emphasis has been given to soil physical parameters despite the perceived importance of aggregation on crop growth, water relations and erosion. In one long-term, cereal-based trial from Syria, four representative crop sequences were selected as they have varying influence on soil organic matter (SOM) levels, e.g., fallow, continuous wheat (Triticum turgidum var durum), vetch (Vicia sativa), and medic (Medicago spp.). These rotations showed increased aggregate stability as SOM increased. Our study examined water-stable aggregates from these rotations at the micromorphological level using the polarizing (on thin sections) and scanning electron microscope. The observations of the influence of SOM at the micro level were inconsistent with those at the macro level as determined by wet sieving. This discrepancy may be related to the age of the SOM and the extent to which organic carbon is intimately mixed with mineral matter. Nevertheless, the changes determined on the shape and porosity characteristics of the water-stable aggregates suggest the value of the micro-scale approach in understanding the mechanism of soil microstructure development. Micromorphology can identify visual details of the physical changes in the evolution of soil microstructure under varying cropping systems. (C) 2007 Published by Elsevier B.V.