There is a public perception that the white-tailed deer Odocoileus virginianus (Artiodactyla: Cervidae) is the main reservoir supporting the maintenance and spread of the causative agent of Lyme disease, Borrelia burgdorferi. This study examines the pathogen prevalence rate of Borrelia in adult Ixodes scapularis (Ixodida: Ixodidae), the black-legged tick, collected from white-tailed deer and compares it with pathogen prevalence rates in adult ticks gathered by dragging vegetation in two contiguous counties west of the Hudson Valley in upstate New York. In both Broome and Chenango Counties, attached and unattached ticks harvested from white-tailed deer had significantly lower prevalences of B. burgdorferi than those collected from vegetation. No attached ticks on deer (n = 148) in either county, and only 2.4 and 7.3% of unattached ticks (n = 389) in Broome and Chenango Counties, respectively, were harbouring the pathogen. This contrasts with the finding that 40.8% of ticks in Broome County and 46.8% of ticks in Chenango County collected from vegetation harboured the pathogen. These data suggest that a mechanism in white-tailed deer may aid in clearing the pathogen from attached deer ticks, although white-tailed deer do contribute to the spatial distribution of deer tick populations and also serve as deadend host breeding sites for ticks.