SynopsisWe described skeletal deformities in Willamette River fishes from larval and juvenile specimens collected in 2002 and 2003. Deformities were found in most taxa examined but were more frequent in native broadcast spawners, especially minnows and suckers, than in native or exotic nest builders. Caudal deformities were uniformly distributed throughout the river, but precaudal deformities were more localized near the towns of Newberg and Salem (Wheatland Ferry). In northern pikeminnow, Ptychocheilus oregonensis, deformities were dependent on relative hatch date, with early season fish having about three times the deformity load as late season fish. In a subsample of northern pikeminnow and chiselmouth, Acrocheilus alutaceus, number of deformities was directly related to number of trematode metacercariae and precaudal deformities were twice as likely as caudal deformities to be associated with metacercariae. Based on a logistic regression, the probability of a precaudal deformity was dependent on number of metacercariae and geographic area with the area effect disappearing as the number of cysts increased. A separate analysis showed that some types of deformities were unlikely to be associated with metacercariae. However, even in cases where metacercariae were unlikely to be associated with deformities, metacercariae were usually present elsewhere in the fish and an indirect effect could not be dismissed. The taxonomic, spatial and temporal patterns of skeletal deformities in Willamette River fishes may be due to differences in intermediate host (snail or fish) resistance or susceptibility to parasites, to differences in life history ecology, or to anthropogenic effects that are manifest in increased precaudal deformities near Newberg and Wheatland Ferry or decreased rates elsewhere.