Nowadays, brain-computer interfaces (BCI) are designed to be used in experimental and clinical studies, and their results allow the creation of new assistive technologies for people with motor disabilities. In 2008, a prototype of a BCI was developed in the School of Engineering of Antioquia and the University CES, which uses electroencephalography (EEG) to record the cognitive P300 evoked potential. In this paper, we propose an experimental and statistical design to compare this BCI prototype with a commercial device (USBamp), studying if they show significant differences or not. At first instance, this study is focused in some tests that characterize the systems, using as input deterministic signals with different values of frequency and amplitude, and which evaluation is made through mean square value, signals spectral density, response time and maximum peak during a stimulus. Secondly, we performed some analog tests in P300 signals evaluating signal energy and latency per channel. We used elements of statistical inference such as: the evaluation of a hypothesis for two means assuming unknown equal variances and equal means tests for two paired samples. According to the evidence, we concluded that the BCI prototype is suitable to measure and process EEG signals, but it is necessary to establish some improvement for certain treatments such as: the design of new circuits to optimize band width.