The biochemistry of plant metabolic pathways has been studied for many generations; nevertheless, numerous new enzymes and metabolic products have been discovered in the last 5–10 years. More importantly, many intriguing questions remain in all areas of metabolism. In this review, we consider these issues with respect to several pathways of lipid metabolism and the contributions made by the Arabidopsis genome sequence and the tools that it has spawned. These tools have allowed identification of enzymes and transporters required for the mobilization of seed storage lipids, as well as transporters that facilitate movement of lipids from the endoplasmic reticulum to the chloroplast in green leaf cells. Genomic tools were important in recognition of novel components of the cutin and suberin polymers that form water-impermeable barriers in plants. The waxes that also contribute to these barriers are exported from cells of the epidermis by transporters that are now being identified. Biochemical and genetic knowledge from yeast and animals has permitted successful homology-based searches of the Arabidopsis genome for genes encoding enzymes involved in the elongation of fatty acids and the synthesis of sphingolipids. Knowledge of the genome has identified novel enzymes for the biosynthesis of the seed storage lipid, triacylglycerol, and provided a refined understanding of how the pathways of fatty acid and triacylglycerol synthesis are integrated into overall carbon metabolism in developing seeds.