Mutations in the Opaque2 (O2) gene of maize (Zea mays L.) improve the nutritional value of maize by reducing the level of zeins in the kernel. The phenotype of o2 grain is controlled by many modifier genes and is therefore strongly dependent on genetic background. We propose two hypotheses to explain differences in phenotypic severity in different genetic backgrounds: (i) Specific genes are differentially (o2 vs. wild-type) expressed only in certain genotypes, and (ii) A set of genes are differentially expressed in all backgrounds, but the degree of differential expression differs in different backgrounds. To determine the extent to which these two hypotheses contribute to determining the severity of o2 in different genetic backgrounds, we identified transcripts likely to be differentially expressed in several genetic backgrounds by transcript profile comparison of endosperm RNA pools from eight o2 inbred lines and their wild-type counterparts. The inbred line B46 was identified as having severe o2 phenotypes while the line M14 was identified as having minimal o2 phenotypes. The degree of wild-type vs. o2 differential expression of transcripts was determined for these two lines. We found that most genes that are downregulated by o2 tend to be differentially expressed to a greater degree in B46 than in M14, while upregulated genes tend to be more highly differentially expressed in one genetic background or the other. Thus, hypothesis one functions more prominently for upregulated genes while hypothesis two functions most prominently for downregulated genes.