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Between 11 May and 27 July 2004, seven hundred and forty- five juvenile fall-run Chinook Salmon (Oncorhynchus tshawytscha) were collected for pathogen and physiological assays at 4 general locations in the lower Klamath River. Pathogens of interest included the bacterium Flavobacterium columnare, and myxozoan parasites Parvicapsula minibicornis and Ceratomyxa shasta. Only 2.4% of fish examined were infected with F. columnare suggesting it was not a significant problem in these fish in 2004. Expanding from trap efficiency data, we estimated that 45% of the population was infected with C. shasta and 94% ofthe population was infected with P. minibicornis:. The high incidence of dual myxozoan infection (98% of Ceratomyxa infected fish), and associated pathology suggests that the majority of the C. shasta infected juvenile Chinook would not survive. The prognosis for P. minibicornis infection by itself is not well understood. Depending on the juvenile Klamath River salmon population size and smolt to adult return ratio, the effective number of adult salmon lost to C. shasta as juveniles could rival the 33,000+ adult salmon lost in the 2002 Klamath River Fish Dieoff.