The genetic organization of the duck circovirus (DuCV) 33753-52 detected in commercial Pekin duck flocks from Long Island, NY, is described. The nucleotide sequence of virus 33753-52 exhibited high similarity with DuCVs previously detected in Germany and Hungary. It is possible that this DuCV from New York shares the same ancestor with the European counterparts. The virus 33753-52 exhibited genetic features characteristic of other circoviruses, such as the presence of two major open reading frames (rep and cap), two intergenic regions, one stem-loop structure, four intergenic direct repeats, and the conserved motifs for the rolling circle replication and for the dNTP binding domain in the Rep protein. This report is the first report of the presence of DuCV in commercial Pekin duck farms in the United States. The clinical and pathologic significance of DuCV in the duck farms located on Long Island needs to be clarified. DuCv was detected in culled birds, due to low body development, leg deformities, or arthritis. Staphylococcus aureus and Riemerella anatipestifer serotype 4 were isolated from some of the DuCV-positive birds. The apparent low prevalence of the virus suggests that at this time, this infection is not a significant problem for the duck industry in New York. However, the immunosuppressive properties of this virus need to be clarified as well as its role as a predisposing agent for other diseases.