We compared the performance and physiological response of diploid and triploid Atlantic salmon (Salmo salar) following 21 days of either unpredictable chronic stress (UCS) or no disturbance (control). Thereafter, all four groups were challenged with a novel acute stressor consisting of crowding, netting and transfer into another tank. Growth was monitored during the 21-day period, and stress response to the novel acute stress challenge was assessed by blood chemistry parameters and pituitary gene expression. Plasma parameters were analyzed before (0) and 15, 30, 45, 60, 90, 120, 240, and 300 min after acute stress induction, whereas gene expression was analyzed at 0, 30, 60, 120, and 240 min. The results showed: a) similar growth rate and condition factor reductions from UCS in triploids and diploids, b) higher post-stress plasma Acth and cortisol levels in triploids compared with diploids, c) wider post-stress fluctuations in most of the other plasma parameters for triploids compared with diploids, particularly for glucose and lactate, d) pomca1, pomcb, crf-r1a and crf-r1b mRNA levels were more upregulated in control diploids than control triploids, and e) only minor changes in pituitary gene expression from UCS in both diploids and triploids, but with a noticeable upregulation of pomca2 and crf-r1a and crf-r1b in the triploids. Our results suggest that triploid Atlantic salmon have a higher energy cost in response to stress than diploids salmon. This can make them more sensitive to suboptimal conditions and episodes of acute and chronic stress.