Different life history stages of juvenile Atlantic salmon around the period of smoltification were subjected to short term stress (confinement) over two sampling years using separate cohorts of hatchery-reared fish. In the first year, confinement stress suppressed subsequent feeding in smolts and post-smolts, but not parr, in association with elevated plasma cortisol levels. Post-smolts showed much lower levels of food intake than either parr or smolts. Plasma ghrelin levels were unaffected by stress in any group. In the second study year, pre-smolts had very low food intake and this was further suppressed following stress. Higher food intake levels in smolts were strongly inhibited post-stress. Both pre-smolts, and smolts showed elevated levels of plasma cortisol and glucose, and suppressed plasma ghrelin levels. Across both study years, stress that was accompanied by elevated plasma cortisol levels resulted in suppression of feeding, whereas a predicted association of suppressed plasma ghrelin levels with reduced food intake, was present only in the second year. The results of the present study indicate that elevated plasma cortisol is a consistent endocrine correlate of stress-suppression of feeding. It is also apparent that the peri-smolt period is associated with markedly reduced feeding in this stock of Atlantic salmon.