Streptomyces scabies causes yield losses in potato by inducing common scab (CS) symptoms on tubers. Little information is available on global gene expression responses in CS-causing streptomycetes upon interaction with host plants. In this study, expression of 8746 genes was analysed in the type strain of S. scabies (ATCC49173) using a custom-designed, gene-specific oligonucleotide microarray. Bacteria were grown in liquid yeast malt extract (YME) medium and 480 genes were found to be up-regulated 24 h after supplementing the cultures with potato microtubers. Quantitative PCR analysis of eight putative or known virulence genes was consistent with the microarray data. Elevated expression of the thaxtomin synthesis gene txtA and txtR genes regulating synthesis of thaxomin A, the main pathogenicity factor of S. scabies, and production of thaxtomin A were detected in cultures containing microtubers. Unexpectedly, thaxtomin was also detected in cultures lacking microtubers, which indicated that growth in YME induces thaxtomin production in S. scabies. Many but not all microtubers incubated in the cultures of S. scabies for 48 h displayed symptoms, indicating that the microtubers were not equally susceptible even though they were produced under uniform in vitro growth conditions. These factors may have limited the differences in gene expression observed between S. scabies exposed to microtubers compared to controls. This study provides some of the first results on the transcriptome of S. scabies, a widely distributed and important potato pathogen, upon exposure to young developing potato tubers. The findings will inform future studies on interactions of CS-inducing streptomycetes with potato and means to control the disease.