A major goal of the Human Genome Project is to establish “ personalized medicine ” on the basis of individual genetic variations. Among the genetic differences present in human populations, polymorphisms in genes that encode various enzymes, transporters, and receptors involved in the metabolism of drugs are considered to be medically important because some can affect therapeutic efficacy of drugs and/or adverse reactions. We have been conducting extensive screening programs to detect genetic variations in the Japanese population. In particular, we seek single-nucleotide polymorphisms (SNPs) in genes of interest by combining direct DNA sequencing with computational analysis. These efforts have allowed us to construct comprehensive SNP maps of 214 gene loci that contain a total of 6845 variations. In this review, we introduce the molecular features of each of those loci, such as regional distributions of SNPs, non-synonymous substitutions, insertion/deletion polymorphisms within coding regions, and other types of variation. This directory for human variations should provide a fundamental molecular basis for understanding the pharmacokinetics or pharmacodynamics of drugs used to treat individual patients.