A wide variety of microorganisms known to produce auxin and auxin precursors form beneficial relationships with plants and alter host root development. Moreover other signals produced by microorganisms affect auxin pathways in host plants. The precise role of auxin and auxin signaling pathways in modulating plant-microbe interactions, however, is unknown. Dissecting out the auxin synthesis, transport and signaling pathways resulting in the characteristic molecular, physiological and developmental response in plants will further illuminate upon how these intriguing inter-species interactions, of environmental, ecological and economic significance, occur. The present review seeks to survey and summarize the scattered evidences in support of known host root modifications brought about by beneficial microorganisms and implicate the role of auxin synthesis, transport and signal transduction in modulating beneficial effects in plants. Finally, through a synthesis of the current body of work we present outstanding challenges and potential future research directions on studies related to auxin signaling in plant-microbe interactions. © 2012 Blackwell Publishing Ltd.