The fast Fourier transform (FFT), has been the main tool for the EEG spectral analysis (SPA). However, as the EEG dynamics shows nonlinear and non-stationary behavior, results using the FFT approach may result meaningless. A novel method has been developed for the analysis of nonlinear and non-stationary signals known as the Hilbert-Huang transform method. In this study we describe and compare the spectral analyses of the EEG using the traditional FFT approach with those calculated with the Hilbert marginal spectra (HMS) after decomposition of the EEG with a multivariate empirical mode decomposition algorithm. Segments of continuous 60-seconds EEG recorded from 19 leads of 47 healthy volunteers were studied. Although the spectral indices calculated for the explored EEG bands showed significant statistical differences for different leads and bands, a detailed analysis showed that for practical purposes both methods performed substantially similar. The HMS showed a reduction of the alpha activity (-5.64%), with increment in the beta-1 (+1.67%), and gamma (+1.38%) fast activity bands, and also an increment in the theta band (+2.14%), and in the delta (+0.45%) band, and vice versa for the FFT method. For the weighted mean frequencies insignificant mean differences (lower than 1Hz) were observed between both methods for the delta, theta, alpha, beta-1 and beta-2 bands, and only for the gamma band values for the HMS were 3 Hz higher than with the FFT method. The HMS may be considered a good alternative for the SPA of the EEG when nonlinearity or non-stationarity may be present.