Change or clean your furnace filter. Replaceable filters cannot be cleaned, but permanent filters can. Spray the permanent filter with a mixture of white vinegar and water to break down dirt and to deodorize the filter. Allow the filter to dry thoroughly before replacing it.
Turn on the furnace and let it run for a few minutes to determine if cleaning or replacing the filter resolved the smell. If the smell is still present, you must rule out other sources of the sewer smell.
Inspect around the drains, faucets and toilets in the rest of the house with the furnace off. Whether your household is on a municipal sewer system or a septic tank, leaks in either system can release gases that can be picked up by your heating system and circulated throughout the home. If you notice a sewer smell around these locations, contact a plumber to resolve the source of the leak.
Schedule a cleaning of the entire duct system of your furnace if you do not find other sources of the sewer smell. While the technician is there, ask him to check for leaks. Leaks in the duct work can draw smells from other areas and pull them into the entire furnace system.