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I am repairing an old motorcycle that has been stationary for 2+ years. I needed to remove the tank and so drained it of fuel (it was about 1/3 full). I then remembered a story about someone doing the same thing and moisture getting into the inside of the tank and it actually rusting. I refilled it with about a cup of fuel.

Does anyone know if this (the rust thing) is actually true?

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The best thing you can do is completely fill it or completely drain it. The reason for this is, it's the fuel that's actually at issue here. Today's fuel with ethanol in it attracts water. If you have the tank completely full, there's no room for the fuel to collect water (there's little surface area for it to absorb the water). If you have it completely empty, there's no fuel and no water to be had. If you are worried about it being empty and rusting, leaving it for a while, spray a bit of WD-40 into the tank. The "WD" in WD-40 stands for Water Displacement. It will keep the water off the inside of the tank and will help prevent corrosion. If you don't overload it with the stuff, when you drop new fuel into the tank, the fuel will cut the WD-40 where it won't interfere with the running of the motorcycle.

In your case leaving a cup of fuel in the tank is a bad thing, as it will absorb water and cause you issues over the long haul.

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