The aim of the present experiment is to evaluate heart rate variability (HRV) and cortisol as indices of mental workload in a complex environment. Heart rate was continuously recorded during flight scenarios that differed in difficulty. The HRV nicely reflected the changes in difficulty. The results support the idea that HRV is a sensitive index for mental workload when tasks are highly demanding and subjects are motivated to exert additional effort whenever the task becomes more demanding. Cortisol was only slightly increased on the experimental day compared to the training day. On the experimental day, post-task levels did not differ from pre-task levels. The level of cortisol in saliva was, however, related to overall task performance. Subjects who had a high level of cortisol had a low level of performance.