A cardiac rhythm management system includes a heart sound detector providing for detection of the third heart sounds (S3). An implantable sensor such as an accelerometer or a microphone senses an acoustic signal indicative heart sounds including the second heart sounds (S2) and S3. The heart sound detector detects occurrences of S2 and starts S3 detection windows each after a predetermined delay after a detected occurrence of S2. The occurrences of S3 are then detected from the acoustic signal within the S3 detection windows.