During work conducted between 2003 and 2006 on the potential for genetically modified cotton to affect soil microbiota it became apparent that variety type can influence microbiology associated with the rhizosphere. To further investigate this we commenced a project to determine the influence of current commercial cotton varieties on their associated rhizosphere microbial populations and functions. Over the duration of the project we have shown that different cotton varieties can significantly influence rhizosphere microbial populations and functions, and we have made some progress into understanding how these differences are brought about. The significance of these observations, with particular reference to reduced or more efficient input systems are discussed. Further research is required before field recommendations can be made.