Chromosome Conformation Capture (3C) is a biochemical technology to analyze contact frequencies between selected genomic sites in a cell population. We have developed a database of manually curated 3C data (3CDB). By searching PubMed and Google Scholar with carefully designed keyword combinations, we have retrieved about 5000 papers, and from which 3319 interactions in 17 species were manually extracted. Moreover, we developed a systematic evaluation scheme for data reliability and classified the interactions into four categories. Our evaluation scheme provides a solution to assess the incomparability of 3C data between laboratories. We believe that 3CDB will be able to provide fundamental information for experimental design and bridge the gap between molecular and systems biologists who must now contend with noisy high-throughput data.