Genetic Analysis Workshop 16 (GAW16) was held on September 17–20, 2008 in St. Louis, Missouri. The focus of GAW16 was on methods and challenges in analysis of single-nucleotide polymorphism data from genome-wide scans. GAW16 attracted 221 participants from 12 countries. The 168 contributions were organized into 17 discussion groups of 6–17 papers each. Three data sets were available for analysis. Two of these were data from ongoing studies, generously provided by the investigators. The North American Rheumatoid Arthritis Consortium provided case-control data on rheumatoid arthritis, and the Framingham Heart Study (FHS) made available information on cardiovascular risk factors for participants in three generations of pedigree data. The third data set included simulated phenotypes for participants in the FHS, using actual pedigree structures and genotypes. This volume includes a paper for each of the 17 discussion groups, summarizing their main findings. Genet. Epidemiol. 33 (Suppl. 1):S1–S7, 2009. © 2009 Wiley-Liss, Inc.