Magneto-encephalography (MEG) was used to examine the cerebral response to affective non-verbal vocalizations (ANVs) at the single-subject level. Stimuli consisted of non-verbal affect bursts from the Montreal Affective Voices morphed to parametrically vary acoustical structure and perceived emotional properties. Scalp magnetic fields were recorded in three participants while they performed a 3-alternative forced choice emotion categorization task (Anger, Fear, Pleasure). Each participant performed more than 6000 trials to allow single-subject level statistical analyses using a new toolbox which implements the general linear model (GLM) on stimulus-specific responses (LIMO-EEG). For each participant we estimated “simple” models [including just one affective regressor (Arousal or Valence)] as well as “combined” models (including acoustical regressors). Results from the “simple” models revealed in every participant the significant early effects (as early as ~100 ms after onset) of Valence and Arousal already reported at the group-level in previous work. However, the “combined” models showed that few effects of Arousal remained after removing the acoustically-explained variance, whereas significant effects of Valence remained especially at late stages. This study demonstrates (i) that single-subject analyses replicate the results observed at early stages by group-level studies and (ii) the feasibility of GLM-based analysis of MEG data. It also suggests that early modulation of MEG amplitude by affective stimuli partly reflects their acoustical properties.