Sorghum is a potential energy crop thanks to its high biomass productivity and low-input requirement. Biomass yield is measured by plant height, maturity and tiller number while grain yield is measured by seed weight. Saccharification yield is the amount of glucose released after enzymatic digestion of biomass. To develop molecular tools for genetic improvement of these yield traits, we measured height, maturity, tiller number, seed weight and saccharification yield of the sorghum mini core collection (Upadhyaya et al. 2009, Crop Science 49:1769–1780) across multiple environments and then used association mapping to map these traits with simple sequence repeat markers. Association mapping identified eight markers associated with maturity/height, six with tiller number, three each with seed weight and saccharification yield. The height/maturity markers were clustered on chromosomes 2, 4, 6, 9, and 10 with previously mapped height/maturity markers/quantitative trait loci (QTLs). The seed weight markers were clustered with seed weight QTLs mapped on chromosomes 2, 3, and 10 (Paterson et al. 1995, Science 269: 1714-1717). Two of the three saccharification markers mapped sorghum genomic regions on chromosomes 2 and 7 that correspond to the maize cell wall and saccharification QTLs mapped by Lorenzana et al. (2010, Crop Science 50:541–555). The marker/QTL regions also contain known gene/homologs that regulate plant height/maturity (Ma1/SbPRR37, FAR1, CRY1, GA2-oxidase and SHI), tiller number (grassy tiller1 and barren stalk1), seed weight (ARF2 and Tag1) and saccharification yield (EgMYB1/ZmMYB31). These markers/genes will be useful for genetic improvements of sorghum as an energy crop.