In this presentation I describe pathway based analyses of genotyping data to identify pathways related to the development of complex diseases, with a focus on lung cancer and selected autoimmune diseases. The goal of this research has been to identify sets of genes that influence disease risk using extensive data that have been developed by collaborative studies. These studies involve research groups from multiple locations across the world, which raises issues about joint analysis of the data. Rather, we adopt an approach in which analyses are performed by center and then merged, to perform first pass meta-analyses. Additionally, we apply novel approaches to organizing the data into pathways while allowing for correlations among markers to reduce discovery of false positive findings. Results from applications to lung cancer and selected autoimmune diseases will be described.