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A quantum theory for the noise of optical pulses in actively mode-locked lasers is presented. In the presence of phase modulation and/or group velocity dispersion, the linear operator that governs the time evolution of the pulse fluctuations inside the laser cavity is not Hermitian (or normal) and the eigenmodes of this operator are not orthogonal. As a result, the eigenmodes have excess noise and the noise in different eigenmodes is highly correlated. We construct quantum operators for the pulse photon number, phase, timing, and frequency fluctuations. The nonorthogonality of the eigenmodes results in excess noise in the pulse photon number, phase, timing, and frequency. The excess noise depends on the frequency chirp of the pulse and is present only at low frequencies in the spectral densities of the pulse noise operators.