The influence of arbuscular mycorrhizal fungi (AMF) on the expression of plant nutrient transporters was studied using a relative, quantitative reverse-transcription polymerase chain-reaction (RQRT-PCR) technique. Reverse-transcribed 18S rRNA was used to standardize the treatments. The technique had high reproducibility and reflected trends in gene expression as observed by Northern blotting. Using this technique, it was demonstrated that both the high-affinity phosphate transporter MtPt2 and a putative nitrate transporter from Medicago truncatula were down-regulated in roots when colonized by some, but not all AMF. Colonization by the AMF Glomus rosea, in particular, failed to strongly down-regulate these plant genes within the root. This technique may be suitable for the study of plant genes in mycorrhizal roots when Northern blotting is not possible due to low gene expression or when limited amounts of tissue are available for study.