A number of leading investigators in Japan have participated in the National Project of Medical Genomics, the so-called ″the Millennium Project″, since April 2000. As for common diseases, such as diabetes, hypertension, cancer, dementia, and allergic disorders, a nation-wide consortium has been organized to perform comprehensive approaches to individual diseases. In concert with ongoing research projects compiling SNPs and microsatellite information, Japanese investigators are planning to perform genome-wide scanning with 100,000 SNPs and 30,000 microsatellites in a case­control study design. Because a number of issues remain to be resolved (e.g., statistical power and significance levels to declare association), a symposium, named ″Hakone-yama symposium″ was held in last November 2001 to discuss practical strategies and ways to avoid the pitfalls of random screening with authorities in the relevant fields. The arguments include: (1) efficient study designs and statistical analysis, (2) lessons from distinguished achievements in the genetics of multifactorial diseases, and (3) a research trend towards the ″post-sequencing era″ .