Is it OK to spray carb cleaner in the carbs of your motorcycle to clean them out while it is running?

Carb cleaner doesn't really clean anything when you spray it down the throat of the carburater. The parts that need cleaning are the jets and internal lines. The only way to truly clean those parts is to remove the carbuater, disassemble it and clean the parts. Some carb cleaners can make a little difference if you run them through the tank, but spraying down the throat only gets a little surface carbon off, if that.

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The main reason to spray OTMAN carb cleaner at a carb while the bike is running to check for a vacuum leak. If you hear any change in the engine noise when you spray carb cleaner at the joint between the carb and the head, then you've got a vacuum leak. Get a new carb-to-head gasket.