Loblolly pine (Pinus taeda L.) is the most widely planted tree species in the USA and an important tree in commercial forestry world-wide. The large genome size and long generation time of this species present obstacles to both breeding and molecular genetic analysis. Gene discovery by partial DNA sequence determination of cDNA clones is an effective means of building a knowledge base for molecular investigations of mechanisms governing aspects of pine growth and development, including the commercially relevant properties of secondary cell walls in wood. Microarray experiments utilizing pine cDNA clones can be used to gain additional information about the potential roles of expressed genes in wood formation. Different methods have been used to analyze data from first-generation pine microarrays, with differing degrees of success. Disparities in predictions of differential gene expression between cDNA sequencing experiments and microarray experiments arise from differences in the nature of the respective analyses, but both approaches provide lists of candidate genes which should be further investigated for potential roles in cell wall formation in differentiating pine secondary xylem. Some of these genes seem to be specific to pine, while others also occur in model plants such as Arabidopsis, where they could be more efficiently investigated.