Blood cells from two unrelated individuals whose erythrocytes exhibit respectively N S-s-U- and MN S-s-U- blood group phenotypes were examined by immunoblotting, periodic acid-Schiff (PAS) staining, and Southern blotting. Protein bands characteristic of delta glycophorin (glycophorin B) were absent from the immunoblots of whole erythrocyte lysates when probed with polyclonal glycophorin antisera and from isolated erythrocyte membranes stained with PAS reagents. Genomic DNA from the two individuals' leukocytes was digested with a panel of restriction enzymes and probed with alpha M glycophorin cDNA obtained from human K562 leukemic cell line. The EcoRI, PstI, and KpnI restriction site patterns were identical to those of S+s+U+ controls in fragment numbers and relative size but differed from controls in band intensities. Restriction mapping with HindIII, PvuII, SacI, MspI, and BamHI revealed that S-s-U- individuals lack fragments that are reproducibly observed in S+s+U+ controls, and most likely encode delta glycophorin. Using truncated 5' and 3' cDNA segments as probes and comparing, in control individuals, hybridization intensities of fragments with amino acid sequence homologies, we have inferred the assignment of restriction fragments to the alpha and delta glycophorin genes. Our results suggest that the absence of delta glycophorin in the two S-s-U- individuals is a result of deletion of the entire delta glycophorin gene. This is the first report of a glycophorin gene deletion.