Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum, is a slowly progressing disease that threatens salmon conservation and restoration programs in North America. The purpose of this study was to track naturally occurring R. salmoninarum infection in representative, Michigan, USA, salmonid stocks using nested polymerase chain reaction (nPCR), quantitative enzyme-linked immunosorbent assay (Q-ELISA), and culture. The Q-ELISA test detected 67.6% infection prevalence, which is lower than culture (77.2%) or nPCR (94.2%), yet it provided semiquantitative data on infection intensity. The disagreement in results among the three assays may reflect the different phases of R. salmoninarum infection at the time of sampling. The testing results demonstrated the presence of six patterns, with each of the patterns representing a probable stage along the course of natural R. salmoninarum infection. Findings also suggest that fish stocks tested in this study were not uniform in the distribution of the diagnostic patterns and that, from studying such patterns, one can determine the course of BKD infection in a particular population.