When I turn on the hot water I hear a thumping or low banging noise which lasts for about a minute and will repeat after a few hours when the hot water is used. This only happens when hot water is first used. I have checked the unit and at this time the unit is not heating water nor has ignition occurred nor is the burner lighted. There is no sound when the hot water is turned off. (“Rapid closing of faucets or solenoid valves in automatic water using appliances can cause a banging noise heard in water pipes”).

I have drained the tank and no sediment appears in the water removed and discarded.
I have opened the release valve and it works normally releasing clean water in the drain.
It is not a rattling noise, which I understand is normal.
I have checked the flue baffle & hanger, and it is not generating any noise and is in good condition. We purchased the unit on 3/23/03 so it is less than 6 years old.

The cold water rush to the bottom of the tank can sometimes cause a low sounding noise on some heaters. It is not something that can be cured with a water hammer eliminator. Since it is not from the pipe itself I do not believe there is a cure with the exception of replacement. My 40 gallon gas unit here has the same or similar problem but it is located away from the living area so you do not hear it unless you are in the same room as the water heater when it happens. Other than the noise the unit works fine.