Harmonic tone complexes with component phases, adjusted using a variant of a method proposed by Schroeder (IEEE Trans Inf Theory 16: 85-89, 1970), can produce pure-tone masked thresholds differing by more than 20 dB. This phenomenon has been qualitatively explained by the phase characteristics of the auditory filters on the basilar membrane which differently affect the flat envelopes of the Schroeder-phase maskers. We examined the influence of auditory-filter phase characteristics on the neural representation in the auditory cortex by investigating cortical auditory evoked fields (AEF). We found that the P1m component exhibited larger amplitudes when a long-duration tone was presented in a repeating linearly downward sweeping (Schroeder positive, or m₊) masker than in a repeating linearly upward sweeping (Schroeder negative, or m_-) masker. We also examined the neural representation of short-duration tone pulses presented at different temporal positions within a single period of three maskers differing in their component phases (m₊, m_-, and sine phase m₀). The P1m amplitude varied with the position of the tone pulse in the masker and depended strongly on the masker waveform. The neuromagnetic results in all cases were consistent with the perceptual data obtained with the same stimuli and with results from simulations of neural activity at the output of cochlear preprocessing. These findings demonstrate that phase effects in peripheral auditory processing are accurately reflected up to the level of the auditory cortex.