Avalanche dogs are specially trained to use their sensitive sense of smell to find buried people in avalanches. Emotional and physical stress factors before and during a search, as well as nervousness felt by the dog handler, negatively influence the efficiency of search dogs. To improve the performance of avalanche dogs and to enable the dogs to operate over longer time periods, a better understanding of the physiological consequences of possible arousal, disturbance and stress occurring during a search mission are needed. In this study faecal glucocorticoid metabolites were analysed. Faecal samples from privately owned avalanche dogs (n = 11) of different breed and age before, during and after 2 separate training camps, each 1 week in length, were collected and the results combined. An enzyme-immunoassay to analyse faecal cortisol metabolites was used to evaluate the stress response during training and search. Compared to baseline concentrations (measured during the weeks before and after the training camp, when dogs were at home), cortisol metabolites increased when dogs were in the training camp. The type of activity in the training camp influenced stress hormone levels significantly (Friedman test, p < 0.001). In descending order, helicopter flights, actual training and the days of arrival/departure caused levels to rise, but there was no significant difference between basal cortisol metabolite concentrations and resting days in the camp. In a real emergency, an experienced dog did show a 2.5 times increase in cortisol metabolite concentration, but 12 h later levels had returned to normal. Age, temperament in terms of being prone to stress, as well as previous experience with training camps were considered to be important factors influencing cortisol metabolite concentrations. Basal hormone levels were significantly and positively correlated with a temperament more prone to stress (r = 0.817, p = 0.002). The number of previously attended training courses affected mean cortisol metabolite concentrations during training, but the observed negative correlation was statistically not significant. A questionnaire was used to investigate whether the dog handlers could realistically estimate the arousal and amount of stress the dogs were exposed to. However, no correlation was found between faecal cortisol metabolites and the estimated stress, indicating that handlers overestimated the amount of stress for the dogs most of the time. In summary results of this study indicate that experience and training are the primary factors in reducing stress during search missions in avalanche dogs.