Confinement of juvenile Atlantic salmon Salmo salar from four different populations (all-female diploids, all-female triploids, mixed sex diploids and mixed sex triploids) either before (FW parr) or after (SW smolts) transfer to sea elevated plasma cortisol and plasma lactate from control levels irrespective of ploidy status. Both before and after confinement, plasma cortisol levels in SW smolts (6-174 ng ml-1) were higher than those in FW parr (4-58 ng ml-1), which possibly reflected the physiological challenge of acclimation to SW. Mixed sex populations of SW smolts had higher cortisol levels than all-female populations. The duration of confinement (1, 3 or 6 h) affected the magnitude of the plasma cortisol and lactate responses in SW smolts. Plasma cortisol levels in diploid and triploid SW smolts subjected to 2 h of confinement decreased to pre-stress levels within 6 h post-confinement. Plasma lactate levels were not significantly different from pre-stress levels 48 h after confinement. As no difference exists in primary and secondary stress responses of Atlantic salmon of differing ploidy status, it is unlikely that differences in mortality rates between diploid and triploid populations under commercial conditions can be attributed to differences in their physiological responses to periods of stress lasting up to 6 h. (C) 2000 The Fisheries Society of the British Isles.