The case-control analyses group focused on a diverse set of questions, including study design, power, and analysis of case-control studies. Papers on study design examined various case-selection strategies, as well as ways to combine information from family- and population-based case-control data. The power of various approaches to case-control analyses was compared in several papers, while two papers chose to apply specific methods to analyzing the data. Two groups examined haplotype-related issues, including resolving unphased haplotypes and comparing haplotype- and single-nucleotide polymorphism-based methods for analyzing data. Finally, one group examined the optimal number of markers for the genomic control approach to population stratification. Genet. Epidemiol. 29(Suppl. 1):S86–S90, 2005. © 2005 Wiley-Liss, Inc.