Pigs from four farms were slaughtered at two abattoirs, each with two slaughter handling systems. Pigs at abattoir X were electrically stunned, either in a floor pen holding five pigs or in a race-restrainer. At abattoir Y pigs were stunned either in a floor pen holding five pigs or in a dip-lift carbon dioxide stunner. At exsanguination, 96 blood samples (24/farm) were collected from pigs slaughtered through each slaughter handling system (384 samples in total). Serum samples were analysed for cortisol, creatine phosphokinase (CPK) lactate dehydrogenase (LDH) and LDH-isoenzymes. There were no significant differences between the systems at abattoir X. At abattoir Y, pigs slaughtered through the floor pen system had higher levels of LDH-5 (39.84 +/- 1.39 per cent of total LDH vs 34.76 +/- 1.21 per cent, P < 0.05) indicating greater skeletal muscle damage in the floor pen. Pigs at abattoir Y had higher mean serum levels of CPK than pigs at abattoir X (3.63 log10 U/litre vs 3.41 log10 U/litre, 0.03 sed, P < 0.001), higher total LDH activities (1269.5 U/litre vs 922.8 U/litre, P < 0.001) and higher cortisol concentrations (1.70 log10 ng/ml vs 1.51 log10 ng/ml, P < 0.001). These differences suggested that the levels of physical and psychological stress were higher at abattoir Y.