Abstract The molecular mechanisms underlying the development and progression of sugarcane mosaic virus (SCMV) infection in maize are poorly understood. A transcript profiling study based on maize unigene-microarrays was conducted to identify genes associated with SCMV resistance in the near-isogenic line (NIL) pair F7 + (SCMV resistant) and F7 (susceptible). Altogether, 497 differentially expressed genes were identified in 4 comparisons addressing constitutive genetic differences, inducible genetic differences, compatible reaction, and incompatible reaction. Compared to a suppression subtractive hybridization (SSH) approach on the same materials, expression patterns of microarray-ESTs and SSH-ESTs were consistent for the same comparisons despite technical discrepancies. Pathogen-induced transcripts were underrepresented on the unigene-microarray, consequently fewer microarray-ESTs (45.8%) were classified into pathogenesis-related categories than SSH-ESTs (60.5%). Moreover, fewer microarray-ESTs (4) co-segregated with Scmv QTL than SSH-ESTs (18). However, our results demonstrate that the microarray experiments complement the SSH-macroarray studies. Good candidate genes (CGs) associated with SCMV resistance can be chosen from three classes: (i) positional CGs co-localized with major Scmv QTL, (ii) functional CGs exhibiting the homology to pathogenesis-related genes, or (iii) differentially expressed ESTs showing consistent expression pattern in both approaches.