Carboxylesterases are a broad class of enzymes important in the detoxification of many ester- or amide-bond containing xenobiotics. They also activate analgesics, anticancer prodrugs, and other biologically active compounds, such as cocaine and heroin. The objective of this work was to identify the CES2 gene structure, complex 5' untranslated regions and three potential promoters for the initiation of transcription in different human tissues. Using bioinformatics and progressive reverse transcriptase-polymerase chain reaction, we found that the 5' untranslated region is more than 1100 bases longer than previously reported. Rapid amplification of cDNA ends showed three distinctive transcription start sites at -74, -629 and -1187. DNA fragments upstream of each of the three transcription start sites were found to be transcriptionally active in HepG2 cells. The distal promoter is active in both orientations, suggesting its potential role in the transcription of another gene, CGI-128, located immediately upstream to the distal promoter in the opposite direction with respect to CES2. Hybridization analyses showed that CES2 is highly expressed in the heart, skeletal muscle, colon, spleen, kidney and liver, but considerably less expressed in fetal tissues (e.g. fetal heart, kidney, spleen, and liver) and cancer cells. It is also evident that the distal promoter is responsible for low level expression of the gene in many tissues, whereas the other two promoters are tissue specific. These findings shed some light on CES2 gene regulation, a gene important in the metabolism of many drugs.