In spite of its great potential, the introduction of genetically engineered microorganisms (GEMs) into soil for agricultural purposes still faces several problems impeding success. Such problems are on one hand related to a lack of establishment and persistence of introduced microorganisms in soil, and on the other hand to putative hazards of introduced microorganisms carrying heterologous genes entering the environment. In this review, the dynamic processes which take place in soil following the introduction of a GEM and which determine both the effectiveness and the putative biohazard, are discussed. Thus, inoculant establishment, survival and transport, gene expression and gene transfer in soil are briefly reviewed as they are influenced by soil factors and mode of inoculation. In addition, the need to use a combination of plating, immuno and molecular (DNA) detection techniques is stressed to provide adequate information on the fate of introduced GEMs and their DNA.