Baylisacaris procyonis is a roundworm that is tolerated by its primary host, raccoons (Procyon lotor). However, this roundworm can be fatal to intermediate mammalian hosts and may be a contributing factor to population declines of the endangered, Allegheny woodrat (Neotoma magister). We used fecal flotation to determine the prevalence of B. procyonis eggs in raccoon scat found in locations that overlap with where woodrats persist in the mid-Atlantic. We determined that B. procyonis was present at two extant woodrat colonies in Maryland and Pennsylvania. We expect woodrat populations at these sites to decline, if the roundworm and other factors (e.g., forest fragmentation) are not alleviated.