Native listeners process and understand homophones, such as la locution ‘the phrase’ vs. l'allocution ‘the speech’, both [lalɔkysjɔ̃], without much semantical ambiguity in connected speech. Yet, behavioral experiments show that disambiguation is partial under intra-speaker variability without semantical context. To investigate electrophysiological correlates of perception of non-contrastive subphonemic features in French homophonous sequences, we examined the event-related potential Mismatch Negativity (MMN) using a multitoken stimuli oddball paradigm. Stimuli were taken from multiple natural productions of nominal homophonous utterances. In the first experiment, we used the first syllables, while in the second experiment, the whole utterances.The homophonous sequence elicited an MMN response in both experiments. This suggests that non-contrastive acoustic features that differentiate homophones, such as pitch and duration, are robust enough despite intra-speaker variability to allow listeners to automatically extract regularities associated with each utterance. This ability of the perception system might contribute to correct segmentation and comprehension of ambiguous utterances.