Experiments were designed to examine the effects of various temperature challenges on oxygen consumption and ammonia excretion rates and protein utilization in juvenile Atlantic salmon Salmo salar. Fish acclimated to 15° C were acutely and abruptly exposed to either 20 or 25° C for a period of 3 h. To simulate a more environmentally relevant temperature challenge, a third group of fish was exposed to a gradual increase in temperature from 15 to 20° C over a period of 3 h (c. 1·7° C h−1). Oxygen consumption and ammonia excretion rates were monitored before, during and after the temperature shift. From the ammonia excretion and oxygen consumption rates, protein utilization rates were calculated. Acute temperature changes (15–20° C or 15–25° C) caused large and immediate increases in the oxygen consumption rates. When the temperature was gradually changed (i.e. 1·7° C h−1), however, the rates of oxygen consumption and ammonia excretion were only marginally altered. When fish were exposed to warmer temperatures (i.e. 15–20° C or 15–25° C) protein use generally remained at pre-exposure (15° C) levels. A rapid transfer back to 15° C (20–15° C or 25–15° C) generally increased protein use in S. salar. These results indicate that both the magnitude and the rate of temperature change are important in describing the physiological response in juvenile salmonids.