Members of the KNOX gene family have important roles in plant meristems by regulating cell division and differentiation. BREVIPEDICELLUS (BP), one of seven KNOX genes in Arabidopsis, has a primary role in internode patterning. We carried out a comparison of RNA expression profiles between wild-type seedlings and bp mutants at a developmental stage prior to a visible phenotypic difference. Transcript differences were found for a number of genes in cell wall biosynthesis, especially genes in the lignin pathway. The regulation of lignin biosynthesis by BP was demonstrated by observing increased lignin deposition in bp mutants following bolting, decreased lignification in plants overexpressing BP, and aberrant lignin deposition in discrete regions of the bp stem. Furthermore, we showed that BP binds promoters of some genes in the lignin pathway. Our results provide a metabolic fingerprint for BP and identify the lignin pathway as one of the coordinate processes that BP regulates.