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Background Salt tolerance in grapevine is associated with chloride (Cl−) exclusion from shoots; the rate-limiting step being the passage of Cl− between the root symplast and xylem apoplast. Despite an understanding of the physiological mechanism of Cl− exclusion in grapevine, the molecular identity of membrane proteins that control this process have remained elusive. To elucidate candidate genes likely to control Cl− exclusion, we compared the root transcriptomes of three Vitis spp. with contrasting shoot Cl− exclusion capacities using a custom microarray. Results When challenged with 50 mM Cl−, transcriptional changes of genotypes 140 Ruggeri (shoot Cl− excluding rootstock), K51-40 (shoot Cl− including rootstock) and Cabernet Sauvignon (intermediate shoot Cl− excluder) differed. The magnitude of salt-induced transcriptional changes in roots correlated with the amount of Cl− accumulated in shoots. Abiotic-stress responsive transcripts (e.g. heat shock proteins) were induced in 140 Ruggeri, respiratory transcripts were repressed in Cabernet Sauvignon, and the expression of hypersensitive response and ROS scavenging transcripts was altered in K51-40. Despite these differences, no obvious Cl− transporters were identified. However, under control conditions where differences in shoot Cl− exclusion between rootstocks were still significant, genes encoding putative ion channels SLAH3, ALMT1 and putative kinases SnRK2.6 and CPKs were differentially expressed between rootstocks, as were members of the NRT1 (NAXT1 and NRT1.4), and CLC families. Conclusions These results suggest that transcriptional events contributing to the Cl− exclusion mechanism in grapevine are not stress-inducible, but constitutively different between contrasting varieties. We have identified individual genes from large families known to have members with roles in anion transport in other plants, as likely candidates for controlling anion homeostasis and Cl− exclusion in Vitis species. We propose these genes as priority candidates for functional characterisation to determine their role in chloride transport in grapevine and other plants. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0273-8) contains supplementary material, which is available to authorized users.