Motor Imagery-based Brain-Computer Interfaces (MI-BCIs) are neurotechnologies that exploit the modulation of sensorimotor rhythms over the motor cortices, respectively known as Event-Related Desynchronization (ERD) and Synchronization (ERS). The interpretation of ERD/ERS is directly related to the selection of the baseline used to estimate them, and might result in a misleading ERD/ERS visualization. In fact, in BCI paradigms, if two trials are separated by a few seconds, taking a baseline close to the end of the previous trial could result in an over-estimation of the ERD, while taking a baseline too close to the upcoming trial could result in an underestimation of the ERD. This phenomenon may cause a functional misinterpretation of the ERD/ERS phenomena in MI-BCI studies. This may also impair BCI performances for MI vs Rest classification, since such baselines are often used as resting states. In this paper, we propose to investigate the effect of several baseline time window selections on ERD/ERS modulations and BCI performances. Our results show that considering the selected temporal baseline effect is essential to analyze the modulations of ERD/ERS during MI-BCI use.