Fish commercial transport is an ordinary practice in the aquaculture industry. This study aimed to investigate the effect of a 48 h transport stress on stress response of meagre ( ) juveniles. Radioimmunoassay (RIA) and Real-Time PCR were used to evaluate muscle cortisol levels and to assess glucocorticoid receptor ( ) gene expression in fish muscle and liver, respectively. Presence and localization of various oxidative stress markers were investigated in different tissues by immunohistochemistry. A significant increase in muscle cortisol levels was observed after loading but a significant decrease occurred after 16 h from departure even without returning to control levels. Molecular analysis on stress response revealed an increase in muscle expression after fish loading that started decreasing during the travel returning to the control level at the end of the transport. Instead, no differences in liver expression were observed along the different sampling points. Immunostaining for heat shock protein 70 (HSP70), 4-hydroxy-2-nonenal (HNE), nitrotyrosine (NT) and 8-hydroxy-2'-deoxyguanosine (8-OHdG) antibodies was detected in several organs. Notably, a higher NT immunostaining intensity was evident in skin and gills of the transported animals with respect to controls. Results demonstrated that cortisol and are useful indicators of stressful conditions in transported fish.