Regardless of the considerable advances towards an optimal brain-computer interface (BCI), this remains inaccurate, unreliable and slow . As a result, the use of other electrophysiological signals have been proposed. For the improvement of motor imagery (MI) based BCIs, the use of the heart rate variability (HRV) has been proposed being that MI activates vegetative mechanisms. This study set out with the aim of answering the following question: Is HRV significantly modified by MI-related control tasks, in comparison with other sensory-cognitive tasks which a BCI user must deal with? For this purpose, time and frequency domain parameters of the HRV estimated from eleven participants, who exposed to nine scenarios with different levels of difficulty, were analysed. Despite its exploratory and interpretative nature, this study offers some insight into the HRV throughout the user-system adaptation of a MI-based BCI system, raising two points: (1) HRV is not only subject to MI activity, but also to other sensory-cognitive tasks undertaken in the course of the brain-computer adaptation process, and (2) we consider that heart rate can be more useful to detect the cognitive state of the BCI user, than to improve the BCI performance as a discriminatory parameter.