Triticale, a man-made interspecific hybrid, is a high yielding crop with excellent adaptability to different environments. We use it as a model system for all the other cereals grown in Canada for development of cellulosic ethanol from its straw. A catalogue of cell wall biosynthesis related genes and their corresponding expression profiles is crucial for understanding the cell wall formation toward the development of the most efficient strategies to optimize production of cellulosic ethanol. Within this project, we have sequenced six stem cDNA libraries from three different genotypes and two developmental stages which yielded more than 6.5 millions of reads.  From those, we have identified ~20,000 reads homolog to rice and maize cellulose and lignin biosynthesis pathways.  Based on the distribution of the NCBI wheat EST dataset, we analyzed the differential expression of genes in different members of the cell wall genes. We also compared the expression pattern of identified cell wall sequences from triticale and their orthologues from maize and found similarities in their expression levels. The expression pattern of three CAD genes, one MYB and one NAC genes in triticale stems was further validated by qPCR. Our results show that these genes were highly expressed at heading stage but were barely activated 2 weeks after flowering. Profiling results of these genes matched the 454 transcriptome sequencing data and was correlated with the cell wall lignifying process observed in maturing triticale stems.