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A PCR assay of 43 acute-phase serum samples was evaluated as a method for early detection of human granulocytic ehrlichiosis (HGE) and determination of etiology when serologic testing is inconclusive. Sequenceconfirmed products of the HGE agent were amplified from three individuals residing or having exposure history in Minnesota or Wisconsin, and similarly confirmed products from Ehrlichia chaffeensis were amplified from three individuals from Florida or Maryland. Etiology, as determined by PCR and serology, was the same whenever there was a fourfold difference between the maximum titers of antibodies to both antigens, indicating that presumptive determination of etiology may be based on fourfold differences in titers. PCR testing determined that E. chaffeensis was the etiologic agent for one individual who had similar titers of antibodies to both agents. PCR assay of acute-phase serum in the absence of whole blood specimens may be a useful method for early detection of human ehrlichiosis and determination of etiology when serologic testing is inconclusive.