Salivary alpha-amylase (sAA) has been proposed as a marker for activity of the sympathetic nervous system (SNS). Recent studies in support of this hypothesis have led to an increased number of researchers integrating amylase measurements into their study designs. Salivary alpha-amylase is produced locally in the salivary glands, controlled by the autonomic nervous system. This entails some methodological consequences and potential pitfalls that might lead to increased error variance and thus prevent successful testing of hypotheses. The goal of this review is to summarize basic and recent findings on methodological issues and potential factors influencing sAA measurement, and to derive a set of recommendations enabling researchers to successfully using sAA in psychoneuroendocrinological experiments.