In this study, post-smolt male Atlantic salmon, previously identified as low (LR) or high responders (HR) based on post-stress cortisol levels, had their head kidney and liver sampled at 12 and 20°C prior to injection (time 0) and after (i.e., at 12 and 24 hpi, respectively) they were injected with either Forte Micro (a multi-valent vaccine containing bacterin, to capture peak antibacterial responses) or an equal volume of phosphate-buffered saline (PBS). Real-time quantitative polymerase chain reaction (qPCR) was then used to measure the expression of 15 biomarker genes in the head kidney and 12 genes in the liver at each temperature/sampling point. Target transcripts were chosen that were related to growth, stress and innate antibacterial immune responses. Many temperature, phenotype and injection effects were found for individual genes within these 3 broad categories, and multivariate statistical analyses (i.e., PCA and PERMANOVA) were used to look for overall patterns in transcript expression. These analyses revealed that HR salmon at 20°C mounted a more robust response (p < 0.05) for the 10 head kidney immune-related transcripts when injected with Forte Micro than LR salmon. In contrast, the 7 liver stress-related transcripts displayed a greater response (p = 0.057) in LR vs. HR fish with Forte Micro at 12°C. Overall, while this research did find some differences between LR and HR fish, it does not provide strong (conclusive) evidence that the selection of a particular phenotype would have major implications for the health of salmon over the temperature range examined.