Systems, methods, and computer program products for frequency-domain estimation of latency between audio signals. In some embodiments, the estimation is performed on first blocks of data indicative of samples of a first audio signal and second blocks of data indicative of samples of a second audio signal, and includes determining a coarse latency estimate, including by determining gains which, when applied to some of the second blocks, determine estimates of one of the first blocks, and identifying one of the estimates as having a best spectral match to said one of the first blocks. A refined latency estimate is determined from the coarse estimate and some of the gains. Optionally, at least one metric indicative of confidence in the refined latency estimate is generated. Audio processing (e.g., echo cancellation) may be performed on the frequency-domain data, including by performing time alignment based on the refined latency estimate.