The rapid development of agricultural biotechnology and release of new transgenic plants for agriculture has provided many economic benefits, but has also raised concern over the potential impact of transgenic plants on the environment. Considerable research has now been conducted on the effects of transgenic plants on soil microorganisms. These effects include unintentional changes in the chemical compositions of root exudates, and the direct effects of transgenic proteins on nontarget species of soil microorganisms. Most studies to date suggest that transgenic plants that have been released cause minor changes in microbial community structures that are often transient in duration. However, due to our limited knowledge of the linkage between microbial community structure and function, more work needs to be done on a case-by-case basis to further evaluate the effects of transgenic plants on soil microorganisms and soil ecosystem functions. This review summarizes the results of a variety of experiments that have been conducted to specifically test the effects of transgenic plants on soil microorganisms, and particularly examines the types of methods that are being used to study microbial interactions with transgenic plants.