The relationship between habitat structural composition, presence of Ixodes scapularis Say (I. dammini Spielman, Clifford, Piesman, and Corwin), and the prevalence of Borrelia burgdorferi infection in small mammal populations was studied at 12 4-ha study sites selected within two perpendicular transects spanning New York State. Species-adjusted small mammal infection rates (SARs) were calculated to enable comparison of B. burgdorferi infection rates among sites with differing small mammal species composition and were used as the outcome variable in a predictive model. Sites with high SARs were characterized by lower overstory tree canopy height and basal area, increased understory coverage, substantial understory shrub coverage, decreased presence of surface water or saturated soil, high dominance values for I. scapularis, and higher tick burdens on small mammals. These differences were statistically significant from sites with moderate or low SAR values. Understory foliage height profiles were created for each study site, and significant differences in vegetation structural composition between high SAR sites and those with low or moderate SAR were documented. High SAR sites had increased density of herbaceous foliage at 0 and 25 cm, and higher shrub density at 0, 25, and 50 cm measurements above the ground, associated with I. scapularis questing success, and lower densities of sapling trees at 25, 50, and 75 cm. The structural composition of understory vegetation may dictate vector density and predict B. burgdorferi infection rates in small mammals in New York State.