IgA has not previously been identified in waterfowl. Studies instead revealed physical and antigenic similarities between duck bile immunoglobulin (Ig) and serum IgM. Here, a differential screening approach was used to clone, from a duck spleen library, the cDNA encoding the heavy (H) chains of IgM and the Ig, identified here as IgA, occurring in duck secretions. Phylogenetic comparisons of inferred amino acid sequences of entire H chain constant (C) regions and of individual domains revealed that the duck mu chain was closest to chicken mu (54% overall identity), and duck alpha was closest to chicken alpha (50% identity). Comparison of the mu and alpha C regions revealed areas of up to 65% amino acid similarity within the C4 domains, accounting for the previously noted antigenic overlap of duck IgM and IgA. Messages for alpha and mu were detected in duck lymphoid organs but the alpha message was most abundant in the respiratory, alimentary and reproductive tracts. The alpha message first appeared around 14 days of age and reached adult levels of expression only at 35-50 days. The results indicate that the duck has a mucosal immune system which utilizes IgA; however, the delayed expression and secretion of duck IgA explains the susceptibility of ducklings to mucosal pathogens. Since the waterfowl are among the most primitive extant birds, the recognition of IgA in the duck supports the conclusion that IgA occurs throughout the class Aves and also existed in the common ancestors of birds and mammals.