The low-frequency intensity modulation in optical transmission systems can occurred by optical performance monitoring or dynamic devices such as acoustooptic tunable filters. Using a conventional receiver model, we derived the optical signal-to-noise ratio (OSNR) and Q penalties due to the low-frequency intensity modulation. The penalty is a function of the extinction ratio, OSNR, the modulation index, and the number of pilot-tone signals. The analytic results show good agreement with the experimental results.