This project aims to present a methodology to study the relationships between physiological measures and evaluation metrics for 3D interaction techniques using methods for multivariate data analysis. Physiological responses, such as heart rate and skin conductance, offer objective data about the user stress during interaction. This could be useful, for instance, to evaluate qualitative aspects of interaction techniques without relying on solely subjective data. Moreover, these data could contribute to improve task performance analysis by measuring different responses to 3D interaction techniques. With this in mind, we propose a methodology that defines a testing protocol, a normalization procedure and statistical techniques, considering the use of physiological measures during the evaluation process. A case study comparison between two 3D interaction techniques (ray-casting and HOMER) shows promising results, pointing to heart rate variability, as measured by the NN50 parameter, as a potential index of task performance. Further studies are needed in order to establish guidelines for evaluation processes based on well-defined associations between human behaviors and human actions realized in 3D user interfaces.