Sera from patients with connective tissue diseases often contain antibodies against snRNA-associated proteins. Using one of these sera in an immunological screening of a human lambda gt11 expression vector cDNA library, two cDNA clones for the U1 snRNP-specific A protein, termed lambda HA-1 and lambda HA-2, were isolated. Monospecific antibodies, eluted from the beta-galactosidase fusion protein of either clone reacted with the U1 snRNP-specific A antigen. The identity of the clones was confirmed by in vitro translation of hybrid selected mRNA. RNA blot analysis revealed a single polyadenylated transcript of about 1.4 kb in human cells. A cDNA of 1.2 kb, isolated from the same lambda gt11 expression library by cross-hybridization with a lambda HA-2 restriction fragment, covered the complete coding sequence of the A protein as demonstrated by in vitro translation of an RNA transcript synthesized from this cDNA. The deduced amino acid sequence contains one very hydrophilic region, and internal sequence duplication and a region highly homologous to the RNP consensus sequence that seems to be common to RNA binding proteins. Sequence comparison with the recently cloned U2 snRNP-specific B" protein revealed two extremely homologous regions located in the carboxy-terminal (homology of 86%) and amino-terminal part (homology of 77%) of the proteins. This structural relationship indicates that proteins A and B", although located in different snRNP particles, may have identical functions.