Estimates of genetic parameters of susceptibility of Atlantic salmon to amoebic gill disease (AGD) were obtained from a bath challenge test with two repeated infections (1612 and 1582 fish, the offspring of 50 sires and 100 dams) and from a field test of their sibs (1156 fish) that were naturally infected and scored once for AGD. A third sibling group were reared in an AGD-free environment and their body weights recorded at harvest. In both challenge tests, susceptibility to AGD were measured using an adapted Taylor gill-score (0–5) where gill-score 3 was divided into three sub-classes 3A, 3B and 3C. In the field test, one gill arch of each animal was swabbed to quantify the amount of Paramoeba perurans by RT-qPCR, and a random sample of 126 of the fish were also analysed by RT-qPCR for Paranucleospora theridion and Branchiomonas cysticola. In the field test, body weights of the fish were recorded at time of gill-scoring and seven months later. In both tests, the distributions of gill-score was quite narrow (large proportion with gill-score 2 and 3A, and none with gill-score 4 and 5). In the field test, average body weight of fish with gill-score 1, 2, 3A and 3B was 17.6, 9.4, 17.9 and 22.2% lower, respectively than fish with gill-score 0. The genetic correlation between gill-score in the bath and the field test was close to zero. Therefore, the present bath challenge test for susceptibility to AGD cannot replace a field test in a selective breeding program. In the AGD-affected environment, the genetic correlation of gill-score with CT was −0.81 ± 0.16 and with body weight − 0.88 ± 0.09. These high genetic correlations indicate that CT and growth may be used as indirect trait measures of susceptibility to AGD. The high genetic correlation between body weights in the AGD-affected and the AGD-free environment (0.86 ± 0.05) indicate a true favourable genetic correlation between susceptibility to AGD and growth in Atlantic salmon. Consequently, selection for increased growth rate will result in a favourable genetic correlated response in susceptibility to AGD. The magnitude of these correlations need to be verified, in particular as the negative effect of decreasing CT-values of P. theridion on body weight was found to be larger than that of P. perurans and that growth of the fish in the AGD-free environment may be affected by other gill pathogens with negative effect of growth.