Rhizomes and tillers grow from underground axillary meristems, which are important determinants of perennial growth habit and architecture in grasses. Leymus cinereus grows from intravaginal axillary meristems (tillers), forming a compact tussock year after year. Conversely, L. triticoides grows from creeping underground rhizomes, capable of forming extensive sods and substantial movement year after year. Homologous and possibly homoeologous QTLs have been detected on LG3a and LG3b chromosomes in the 164-sib TTC1 and 170-sib TTC2 Leymus triticoides x (L. triticoides x L. cinereus) mapping families, using high-density molecular genetic linkage maps with 1583 AFLP markers and 64 anchor loci. In this report, we used the Affymetrix barley and wheat GeneChips to compare RNA expression between intravaginal tiller meristems and horizontally growing rhizome meristems of similar length (i.e. less than 3 cm long), from TTC1 and TTC2 progeny bulks that carry caespitose or rhizomatous LG3a QTL alleles. Approximately 39.9% and 40.2% barley probe sets detected homologous transcripts in the Leymus tiller and rhizome meristems, respectively. A relatively small number of expression polymorphisms were detected in the tiller and rhizome meristems, thus overall gene expression patterns are remarkably similar in these tissues.