A new database, SwePep, specifically designed for endogenous peptides, has been constructed to significantly speed up the identification process from complex tissue samples utilizing mass spectrometry. In the identification process the experimental peptide masses are compared to the peptide masses stored in the database, both with and without possible post-translational modifications. This intermediate identification step is fast and singles out peptides which are potential endogenous peptides and can later be confirmed with tandem mass spectrometry data. Successful applications of this methodology are presented. The SwePep database is a relational database developed using MySql and Java. The database contains 4180 annotated endogenous peptides from different tissues and originates from 394 different species, as well as 50 novel peptides from brain tissue identified in our laboratory. Information about the peptides, including mass, isoelectric point, sequence and precursor protein is also stored in the database. This new approach holds great potential for removing the bottleneck which occurs during the identification process in the field of peptidomics. The SwePep database is available at http://www.swepep.org.