In an audio system having a microphone, a speaker coupled to a source of audio output, and an echo canceller coupled to the speaker and microphone, latency between the source of audio output and the speaker may be compensated in echo cancellation performed by the echo canceller. The echo canceller may use a reference signal derived from a signal from the source of audio output in echo cancellation. The latency may be compensated by measuring the latency between the signal from the source of audio output and the speaker, determining a delay amount from the latency, delaying the reference signal by the delay amount to produce a delayed reference signal, and using the delayed reference signal as the reference signal in the echo canceller.