When clinical specimens of influenza virus are adapted to grow in embryonated hens' eggs, variants are selected which have specific amino acid substitutions in the hemagglutinin (HA). In contrast, a single virus, distinct from any egg-adapted variant, is selected when virus is isolated on MDCK mammalian cell culture. We have utilized the polymerase chain reaction to determine the nature of the hemagglutinin of influenza B viruses present in clinical material prior to cultivation in the laboratory. Sequence analysis of individual clones of amplified DNA reveals that the HA of clinical virus is essentially homogeneous and identical to the virus derived on MDCK cells. The HA of egg-adapted virus was heterogeneous and nonidentical to that of the clinical material and of the MDCK-derived virus.