Introduction: Preliminary studies indicate that trypsin regulates the function of guinea pig pancreatic ducts via activation of proteinase-activated receptors. However, there are no data on the number and characteristics of trypsinogen isoforms expressed in the guinea pig pancreas. Aim: Our aim was to purify and clone the trypsinogen isoforms from the guinea pig pancreas and characterize their activation properties. Methods: Ecotin-affinity chromatography was used for the purification of trypsinogen from pancreatic homogenates. Total RNA was isolated with the RNAqueous kit (Ambion) and reverse-transcribed with the SMART RACE cDNA Amplification Kit (Clontech). Activation properties of trypsinogens were tested with enteropeptidase, cathepsin B and trypsin. Results: Chromatography of pancreatic homogenates yielded a single peak with homogenous N-terminal amino-acid sequence (LPIDD). Cloning of trypsinogen cDNAs revealed two distinct but nearly identical isoforms as the only difference between the two isoforms is a Ser/Ala change at position 15 within the signal peptide. Thus, both cDNA variants give rise to the same mature trypsinogen upon secretion. Guinea pig trypsinogen is readily activated by enteropeptidase and cathepsin B, but exhibits essentially no autoactivation, under conditions in which human cationic and anionic trypsinogens rapidly autoactivate. Discussion: The guinea pig pancreas secretes a single isoform of trypsinogen. The finding is surprising, because other vertebrates studied so far express multiple trypsinogens. Furthermore, the guinea pig trypsinogen is deficient in autoactivation, but may be prematurely activated by cathepsin B under pathologic conditions. The autoactivation defect might explain the scarcity of pancreatitis models using this species. Finally, this study suggests that multiple trypsinogen isoforms and their ability to autoactivate are not required for normal digestive physiology in mammals.