The expression of phenylpropanoid and related genes was investigated in bm1, bm2, bm3, and bm4 near-isogenic maize plants at the 4-5 leaf stage using a gene-specific cell wall macro-array. The bm3 mutant, which is mutated in the caffeic acid O-methyltransferase (COMT) gene, exhibited the lowest number of differentially expressed genes. Although no other phenylpropanoid gene had an altered expression, two distinct OMT and two cytochrome P450 genes were overexpressed suggesting the activation of alternative hydroxylation/methylation pathways. The bm1 mutant had the highest number of differentially expressed genes, all of which were under-expressed. Bm1 mutant plants were affected not only in cinnamyl alcohol dehydrogenase (bm1 related CAD) gene expression as expected, but also in the expression of other CAD/SAD gene family members and several regulatory genes including MYB, ARGONAUTE and HDZip. As originally believed, the bm1 mutation could be localized at the CAD locus, but more probably in a gene that regulates the expression of the CAD gene family. The profile of under-expressed genes in the bm2 mutant is nearly similar to that of bm1. These genes fell under several functional categories including phenylpropanoid metabolism, transport and trafficking, transcription factors and regulatory genes. As the bm2 mutant exhibited a lower guaiacyl (G) unit lignin content, the bm2 mutation could affect a regulatory gene involved, perhaps indirectly, in the regulation, conjugation or transport of coniferaldehyde, or the establishment of G-rich maize tissues. The pattern of gene expression in bm4 plants, characterized by the over-expression of phenylpropanoid and methylation genes, suggests that the bm4 mutation likely also affects a gene involved in the regulation of lignification.