In the post-genome sequencing era, “Structural Genomics” has become one of the most important research fields in life science. Here I introduce the outline of the study of structural genomics in RIKEN Genomic Sciences Center and also the connection between surface science and structural genomics. Structural genomics is an emerging research field, which examines the enormous amounts of information stored in the genomes of living organisms. We are trying to determine a variety of three-dimensional structures of protein mainly by NMR and also to analyze the structure-function relationship of the proteins systematically and comprehensively. In the process of protein function analysis, molecular interaction analysis is very important and we use various methods including in silico screening, mass spectrometry, surface plasmon resonance, NMR, and so on. All of these analytical methods are based on protein-ligand interaction on molecular surfaces.