Much of the research on stereoscopic 3D (S3D) QoE has dealt with the effects of image features over user's visual discomfort. Nevertheless, the relationships between visual discomfort and other high-level perceptual dimensions such as the viewers' emotional reactions have not been yet explored. Since emotions play a key role on media reception processes, and especially in entertainment contents consumption, this question deserves to be thoroughly addressed to improve the design of image processing techniques. This paper raises and investigates the possible relationship between image distortions and its impact on the emotion context of S3D. We implemented an experimental design in which participants watched a series of 3D contents with different levels of visual distortions supposed to induce visual discomfort, while self-reported and psychophysiological measures of emotions were recorded. Results showed that physiological correlates of emotions were affected by visual discomfort conditions, and that these measures were more sensitive than traditional self-reported measures.