We have detected an endoglycosidase activity produced by Flavobacterium meningosepticum. This enzyme, named endo F, cleaves glycans of both the high-mannose and the complex type linked through asparagine to the protein backbone. The data indicate that cleavage occurs via hydrolysis of the glycosidic bond of the N,N'-diacetylchitobiose core structure adjacent to asparagine, similar to that due to endo H and endo D. Extreme variability was noted in the availability of this cleavage site among N-linked glycoproteins. Glycoproteins of retrovirus, lymphocytic choriomeningitis virus, Pichinde virus, and HLA-A and -B antigens were readily cleaved in the presence of nonionic detergent. Others, such as ovalbumin, fetuin, bromelain, ovomucoid, alpha 1-acid glycoprotein, immunoglobulin G, and influenza virus hemagglutinin became susceptible only after reduction and alkylation or when cleavage was performed in the presence of 1% 2-mercaptoethanol. Endo F should prove useful in the study of glycans and protein backbones as discrete entities and for defining the nature of the glycan-protein interface.