Shortnose Sucker (Chasimistes brevirostris) and Lost River Sucker (Deltistes luxatus) are endemic to the Upper Klamath Basin of Southern Oregon and Northern California, and their populations are in decline. We used histopathology and external examination of 140 and external examination only of 310 underyearling suckers collected in 2013, 2015 and 2016 to document pathological changes, particularly those relating to parasites. The most severe infection was caused by a Contracaecum sp., infecting the atrium of 8%-33% of Shortnose Suckers. The most prevalent infections were caused by Bolbophorus sp. metacercariae in the muscle of Shortnose Suckers (21%-63%) and Lernaea cyprinacea in the skin and muscle of Lost River Suckers (30%-81%). Histology detected Bolbophorus in only 5% of cases where it was not seen externally. Three myxozoans were observed; a Parvicapsula sp. in the renal tubules (10%), a Myxobolus sp. in the intestinal mucosa (2%) and an unusual multicellular, presporogonic myxozoan in the intestinal lumen of one sucker. Severe gill epithelial hyperplasia was observed in several fish collected in 2016. Trichodinids and Ichthyobodo sp. were observed on some of the gills, but absent in many of the fish with severe lesions. A histiocytic sarcoma was observed in sucker.