Soil microbial processes are an integral part of soil quality. Soil organisms contribute to the maintenance of soil quality in that they control the decomposition of plant and animal materials, biogeochemical cycling of elements such as C, N, P, S, etc.; the formation of soil structure; and the fate of organics applied to soil. A variety of methods are available to assess the microbial status of a soil. There is still a need, however, for a better understanding of biological soil processes and community structure. Moreover, few attempts have been made to define what should be included in a data set of microbial indicators of soil quality. As a consequence, lacking is a complete data set on the microbial portion of soil quality. The challenge ahead is to define the proper data set so that informed management and regulatory decisions can be made. The indicators the authors choose need to respond to perturbations, accurately assess the functioning of the system, indicate temporal or spatial differences, and be cost effective and relatively rapid. One method will not be adequate for all situations. Each assay is an indicator of some portion of soil biology and needs to be selected with considerations of the purpose of the assessment. The task is to identify the minimal number of biological parameters that consider processes as well as the community diversity for the successful estimation of the role of the biotic component in determining soil quality. These methods also will need to be considered in concert with soil physical and chemical measurements. Soil microorganisms are potentially one of the most sensitive markers available to classify and assess soil quality.