Faba bean (Vicia faba L.) has been little examined from a genetic or genomic perspective despite its status as an established food and forage crop with some key pharmaceutical factors such as vicine and convicine (VC), which provoke severe haemolysis in genetically susceptible humans. We developed next-generation sequencing libraries to maximize information to elucidate the VC pathway or relevant markers as well as other genes of interest for the species. One selected cultivar, A01155, lacks synthesis of the favism-provoking factors, VC, and is low in tannin, while two cultivars, SSNS-1 and CDC Fatima, are wild-type for these factors. Tissues (5- to 6-d-old root and etiolated shoot and developing seed coat) were selected to maximize the utility and breadth of the gene expression profile. Approximately 1.2 × 106 expressed transcripts were sequenced and assembled into contigs. The synthetic pathways for phosphatidylinositol or phytate, the raffinose family oligosaccharides, and proanthocyanidin were examined and found to contain nearly a full complement of the synthetic genes for these pathways. A severe deficiency in anthocyanidin reductase expression was found in the low-tannin cultivar A01155. Approximately 5300 variants, including 234 variants specific to one of the three cultivars, were identified. Differences in expression and variants potentially related to VC synthesis were analyzed using strategies exploiting differences in expression between cultivars and tissues. These sequences should be of high utility for marker-assisted selection for the key traits vicine, convicine, and proanthocyanidin, and should contribute to the scant genetic maps available for this species.