Microbes and plants have evolved and produce a large array of complex secondary metabolites. Secondary metabolites- natural products- are some of the most structurally interesting molecules found in nature, and also serve as effective pharmaceutical agents.Alkaloids, nitrogen containing compounds produced by higher plants, are arguably some of the most chemically complex molecules found in nature, and exhibit a diverse array of potent biological activities. However, the biosynthetic pathways of these molecules are more challenging to elucidate than the polyketide and peptide pathways found in microbial organisms. First, eukaryotic plant hosts are slower growing and developmentally more complex than prokaryotes, and genomic sequence data of medicinal plants are unavailable. Furthermore, the genes of a given metabolic pathway are physically clustered on the genome of a microbial organism; once a fragment of the metabolic pathway has been identified, it is a relatively straightforward process to sequence the adjoining DNA that contains the remainder of the pathway. Plant pathways are generally not clustered, meaning that each plant enzyme of a pathway must be individually isolated and cloned independently of one another. For these reasons, despite the medicinal importance of plant natural products, plant pathways are not as well understood as bacterial natural product pathways.To date, comparatively few enzymes involved in plant alkaloid biosynthesis have actually been cloned, though more enzymes have been purified. Many plant enzymes are characterized by "reverse genetics" in which the enzymes are isolated from plants or plant cell culture by traditional biochemical chromatography techniques. More recently, plant cDNA libraries have been screened for the presence of P450 enzyme or acetyl transferase homologues. If the appropriate DNA libraries or arrays are available, cDNA subtraction techniques can be used to compare the differences in gene expression between alkaloid producing and nonproducing plants. These sequencing and proteomics technologies have been sufficiently refined such that they can be used to address the challenges associated with plant pathways. Therefore, although study of plant alkaloid pathways remains a challenging prospect, modem technologies are beginning to transform the study of plant secondary metabolism.