One of the many controversies surrounding large-scale biofuel production is the diversion of land and other resources that might otherwise be used for food crops. Recent innovations will lead to a second generation of biofuel crops that can co-exist with food crops with little or no competition. Feedstocks from these bio-energy crops will be used to produce liquid fuel from cellulose, the most abundant polymer on the planet. Cell walls of higher plants are mainly composed of cellulose, hemicellulose, and lignin polymers. Cellulose and hemicellulose are polysaccharides with obvious value for biofuel production. However, lignin, while vital for plant growth and development, is widely known to negatively impact conversion efficiencies. Biomass pre-treatment, which is aimed at lignin removal, is not straightforward, and presents one of the major scientific and technical challenges and expenses associated with secondgeneration biofuel production. Scientific breakthroughs associated with altering the expression of key genes in the lignin biosynthetic pathway of biomass crops is a promising path toward solving this problem, and will likely impact the feedstock patent landscape in the near future. This review summarizes some of the recent and most important issued patents and patent applications associated with lignin-modification genes and methods of developing transgenic plants with altered lignin content and composition.