The distribution of genes coding for membrane proteins was investigated in 16 complete genomes: 4 archaea, 11 bacteria, and 1 eukaryote. Membrane proteins were identified by our new method of predicting transmembrane segments () after the removal of amino-terminal signal peptides. Interestingly, about half of the membrane protein genes in each genome were found to be located next to another, forming tandem clusters. Roughly 10%-30% of the tandem clusters were conserved among organisms, and most of the conserved tandem clusters belonged to one of the three functional groups, namely, transporters, the electron transport system, and cell motility. A tandem cluster sometimes contained paralogous membrane proteins, in which case the cluster size and the number of transmembrane segments could be related to a functional category, especially to transporters. In addition to the clustering of membrane proteins, the clustering of membrane proteins and ATP-binding proteins in the complete genomes was also analyzed. Although this clustering was not statistically significant, it was useful to identify candidate membrane protein partners of isolated ATP-binding protein components in the ABC transporters. Possible implications of tandem cluster organization of membrane protein genes are discussed including the complex formation and other functional coupling of protein products and the mechanism of protein translocation to the cell membrane.