Considerable effort and expense has been expended in attempts to detect specific polymorphisms in genetic loci contributing to susceptibility to allergic diseases. Increasingly, 'intermediate' phenotypes for asthma and other allergic diseases have become the focus of such investigations, due to disease heterogeneity and the difficulty of defining disease status. Together with meta-analysis of existing linkage datasets and the completion of many second-stage and specialized genome scans, the recent focus in asthma and atopy genetics has been on single nucleotide polymorphism discovery and genotyping in candidate genes.