Ixodes scapularis ticks collected in 2000 and 2001 from sites in northwestern (Erie County) and southeastern Pennsylvania (Chester and Delaware Counties) were tested for Anaplasma phagocytophila and Borrelia burgdorferi using nested PCR assays targeting the 16S rRNA and flagellin (fla) genes, respectively. PCR-amplified products were sequenced to confirm the presence of A. phagocytophila and/or B. burgdorferi DNA. B. burgdorferi DNA was amplified from 162 of 263 ticks (61.6%) collected in Erie County, Pennsylvania (northwest) and from 25 of 191 (13.1%) ticks collected in the southeast Pennsylvania (TABLE 1). DNA sequencing of a 350-bp region of the B. burgdorferi fla gene1 showed that the agents found in the Erie County, Pennsylvania area were very similar to the human pathogenic B. burgdorferi strains B31 and JD1, with greater than 98.0% identity. DNA sequencing of amplicons from samples that were PCR-positive for A. phagocytophila2 revealed the presence of two organisms, the agent known to cause human granulocytic ehrlichiosis (Anaplasma phagocytophila-human agent; AP-ha) and a closely related organism (AP-Variant 1) that has not been associated with human infection. 2, 3 AP-ha was distinguished from AP-Variant 1 based on a two-base difference in the amplified region of the 16S rRNA gene. Whereas AP-ha was the only strain detected in Erie County, Pennsylvania, both organisms were found within a 20-mile radius of Philadelphia, Pennsylvania. Sixty-two of 73 (84.9%) engorged adult ticks collected from more than 25 white-tailed deer in 2000 from southeast Pennsylvania tested