An important aspect of auditory scene analysis is sequential grouping of sounds that are similar to one another in preference to sounds that follow one another. This grouping problem is captured by stream segregation tasks with alternating distinct sounds. We examined human auditory cortex activity with low noise fMRI in a stream segregation experiment relying on timbre differences of alternating harmonic tones (organ-like and trumpet-like). We found that stream segregation performance in comparison to monitoring a non-separable control stream increased activation exclusively in left auditory cortex and particularly in posterior areas. Our results suggest that left auditory cortex is selectively involved in this complex sequential task although the available cue for sequential grouping was timbre, usually attributed to right hemisphere analysis.