Greetings from Mama Duck from Ductz of Greater Atlanta. These are some awesome comments and a few are from high quality duct cleaners that I personally know. After 19 years in this industry I agree that a government agency is not always up to date with their knowledge but won't admit it. If they were out in the field with our technicians every day they would upgrade their info. I get calls all the time where customers have been taken advantage of by "go and blow" companies. The customers don't know what they don't know but many are too lazy to do the research and are just looking for cheap. The industry has gotten a bad rap due to these con artists but the customer has to take some responsibility. I ask them why they would want to do business with a company who lies to them in print? Are they stupid or just cheap? Thankfully there are those of us in the industry who are working diligently to raise the bar on quality, protect the consumer and perform high quality work. At Ductz all our technicians are NADCA certified, trained by the best in the industry and know how to clean the entire system.
In reading through all this about duct cleaning, THE ONE preventative measure people need to realize is that a poorly installed HVAC system that is not sealed and air tight to ensure that ALL indoor air passes through a GOOD air filtration system IS THE best means of ensuring your ducts remain clean. Duct cleaning does not now and will NEVER improve an HVAC systems efficiency. Proper maintenance and installation are the key just as improper installation practices allow for dust infiltration into the duct system. I am a state licensed contractor in Texas, and unless people have their hvac system sealed and/or properly installed, duct cleaning is an absolute waste of money. My duct system is 12 years old as is as clean today as the day I installed the system with ductwork. SO before ANYONE jumps on the bandwagon of duct cleaning, get with your hvac professional FIRST.
There are many interesting comments from several informed individuals. The question that has not been answered is how do duct systems get dusty and dirty? As a RESNET Home Energy Rater, I perform pressure tests on homes and duct systems, and the one common thread is . . . most air delivery sytems have large amounts of air leakage. The solution is to seal the duct system, and pay particular attention to the return duct system and ductwork near the air handler (the 'blower'). As others have said, a captive (sealed) duct system with proper filter maintenance should be more then adequate for most occupants. For those who have allergy, asthma, or other breathing problems, a filter with a higher MERV rating (number should be listed on the package) or a HEPA filter are good choices. These filters will capture smaller particulates and should improve the indoor air quality. Again, make certain that the entire duct system is sealed, preferably with mastic, second choice UL-181 foil tape - never use cloth duct (also known as duck) tape.

The short answer is yes, duct cleaning, done right by a reputable company will help with the smell. It is likely though the smell is coming from another source, ie the crawl space. It could also be that another rodent is dead in the duct work. A visual inspection would be in order to check for any breach in the duct system. A duct pressure test would be able to tell you how much air is leaking from the system over all. A hole large enough for an animal to enter would loses a great deal of air, over 300 CFM. It would be worth looking into having this test done and it should cost around $200. Cleaning the air handler and evaporator coil will greatly improve the performance of the air conditioner. Dirt and dust on the evaporator acts as insulation and reduces the amount of cooling done be the coil. Any quality duct cleaning should include cleaning the air handler and coil, and the tech should allow you to watch him perform the work as it is done.
In some older homes, there was a grey Mylar flexible duct. After years of use, it started to decompose. A duct cleaning company can come out and find why your air is so dirty and why your building doesn’t heat or cool like it used to. This is a savings on your part. You could also be sucking in Hot, dirty attic air. However, sometimes when a duct cleaning company comes out to clean it, the old duct can be destroyed and have to be replaced. Someone with little experience can replace this ductwork but if it isn’t done right it can ruin a lot of things and cost a lot in repairs.
You should be aware that although a substance may look like mold, a positive determination of whether it is mold or not can be made only by an expert and may require laboratory analysis for final confirmation. For about $50, some microbiology laboratories can tell you whether a sample sent to them on a clear strip of sticky household tape is mold or simply a substance that resembles it.
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