The aim of the present review was to evaluate the literature suggesting that consideration be given to the existence of specific microwave (MW) effects on prokaryotic microorganisms; that is, effects on organisms that cannot be explained by virtue of temperature increases alone. This review considered a range of the reported effects on cellular components; including membranes, proteins, enzyme activity as well as cell death. It is concluded that the attribution of such effects to non-thermal mechanisms is not justified due to poor control protocols and because of the possibility that an unmeasurable thermal force, relating to instantaneous temperature (T (i)) that occurs during MW processing, has not been taken into account. However, due to this lack of control over T (i), it also follows that it cannot be concluded that these effects are not 'non-thermal'. Due to this ambiguity, it is proposed that internal 'micro'-thermal effects may occur that are specific to MW radiation, given its inherent unusual energy deposition patterning.