Allegheny woodrat (Neotoma magister) populations have been in decline across their range since the late 1970s. Hypotheses proposed to explain these declines include habitat fragmentation and loss, decreased food availability, and increased mortality from infection with Baylisascaris procyonis. We investigated the prevalence of B. procyonis at raccoon (Procyon lotor) latrines in woodrat cliff habitats (n=18) along the Ohio River in southern Indiana in 1995. We located 275 latrines (mean=15.3/site; range, 6–34) and found B. procyonis in 13 (4.7%) latrines across all sites. When present at a site, B. procyonis occurred, on average, at 11.1% of latrines (range, 3–36%). Woodrat abundance, determined through a concurrent live-trapping program, was significantly higher (χ²=5.12, df=1, P=0.024) at sites where B. procyonis was not found (9.5±2.52) than at sites with B. procyonis (3.7±2.2). Our analyses support the hypothesis that this parasite could contribute to declines in woodrat abundance. Because woodrats cache nonfood items, including raccoon feces, and are highly susceptible to the parasite, they are at increased risk for B. procyonis infection, which could be deleterious, especially to small populations.