Plant viruses transmitted by the obligate root-infecting plasmodiophorid parasites Polymyxa graminis and Polymyxa betae cause devastating yield losses to cereal and sugar beet crops worldwide. Barley is a non-host for P. betae but is a host for P. graminis. Using the Barley1 GeneChip® microarray we have investigated the transcriptional re-programming of barley roots during the earliest non-host and host interactions with zoospores of these protist species. At high confidence levels we detected 20 and 13 genes with increased transcriptional activity in response to P. betae and P. graminis, respectively, compared to unchallenged barley roots. Functional classification of the induced genes showed that a majority of the genes from both responses were associated with a classic defence response. Validation by quantitative RT-PCR analysis indicated that all of the genes examined were induced to comparable levels in both non-host and host responses. Our results also demonstrated that the barley defence-associated genes, RAR1, ROR1 or ROR2 were not essential for limiting the establishment of P. betae infection in barley. These data suggest that in barley roots the Polymyxa species induce a similar basal defence response whether the interaction is with a non-host or host. Thus, the early response to protist plant parasites appears to be part of the general 'frontline' defence against invading microbes.