We report the presence of a new fatty acyl coenzyme A (acyl-CoA) elongation system in Cryptosporidium and the functional characterization of the key enzyme, a single long-chain fatty acid elongase (LCE), in this parasite. This enzyme contains conserved motifs and predicted transmembrane domains characteristic to the elongase family and is placed within the ELO6 family specific for saturated substrates. CpLCE1 gene transcripts are present at all life cycle stages, but the levels are highest in free sporozoites and in stages at 36 h and 60 h postinfection that typically contain free merozoites. Immunostaining revealed localization to the outer surface of sporozoites and to the parasitophorous vacuolar membrane. Recombinant CpLCE1 displayed allosteric kinetics towards malonyl-CoA and palmitoyl-CoA and Michaelis-Menten kinetics towards NADPH. Myristoyl-CoA (C 14:0 ) and palmitoyl-CoA (C 16:0 ) display the highest activity when used as substrates, and only one round of elongation occurs. CpLCE1 is fairly resistant to cerulenin, an inhibitor for both type I and II fatty acid synthases (i.e., maximum inhibitions of 20.5% and 32.7% were observed when C 16:0 and C 14:0 were used as substrates, respectively). These observations ultimately validate the function of CpLCE1.As one of the vital compounds for all organisms, fatty acids of 14 to 18 carbons in length comprise the bulk of cellular fatty acids that serve structural and biological functions, and they are usually the major products of de novo synthesis in most cells. These long-chain fatty acids play important roles in many biological functions such as energy metabolism and membrane structure. There are several metabolic pathways that produce long-chain fatty acids, most notably the type I and type II fatty acid synthases (FASs). The type I enzymes of mammals and fungi are typically cytosolic and composed of multiple enzymes arranged into domains of one or two large polypeptides (31). In contrast, the enzymes of the type II FASs are all located on separate domains and are found in prokaryotes or in eukaryotic organelles of prokaryotic origin (33).Relatively common among eukaryotic organisms are the fatty acid elongase-based systems. These elongase-based systems directly elongate a fatty acyl chain esterfied with CoA (fatty acyl-CoA), which is in contrast to the type I and type II FAS systems, which elongate a fatty acyl chain attached to an acyl carrier protein. The elongase system is comprised of at least four enzymes that are responsible for adding two carbon units to the fatty acyl carboxyl end. The chemistry of this pathway is similar to that used by type I and type II FASs. Fatty acyl elongation begins with the condensation of malonyl-CoA with a fatty acyl-CoA catalyzed by the condensing enzyme LCE (-ketoacyl-CoA synthase) (Fig.