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 $200. Cleaning the air handler and evaporator coil will greatly improve the performance of the air conditioner. Dirt and dust on the evaporator acts as insulation and reduces the amount of cooling done be the coil. Any quality duct cleaning should include cleaning the air handler and coil, and the tech should allow you to watch him perform the work as it is done.
Furnace cleaners are mostly young men, I know this, I have been one for 15 years or so……so heres the truth, if there are any allergies, children, older people with health issues, we are GOING to make money. do not tell the company you have hired about any health complication. they are salesmen. and they don’t care about you. or your money. make sure they do a good job, then kick them out. you don’t need all the bells and whistles they wanna sell you. any idiot can clean duct work, like I said, I am one of them. I am very good at it, but I don’t have the back bone to sell a widowed old lady a humidifier that she doesn’t need for 500 bucks, overall, if you think you need this service done, which you probably don’t, get it done, do not spend anything over 300$ and do not do it again for at least ten years.
WELL, this summer when I opened them up we had black dust spewing from one of the upstairs vents. It resembled the fuzz that comes off new towels. This prompted us to look into duct cleaning. We heard from someone who had it done several times, said it was worthwhile, and knew of a firm that did a good job. Clean Air America sent a single technician for the appointment and after counting registers and ducts gave me a price of $360.00 which included “sanitizing” the system (a $99 additional fee per can used). The small size of the plenum forced him to connect the 8” round vacuum hose from the truck to the 10” square opening from our humidifier unit. In hindsight, a mistake since it reduced the “negative” pressure in the system.

I am a service technician [since '92].....and as to double filtering.....I have never recommended it. Granted.....it would be noticeably helpful if the fiberglass filters are the main ones used [which I also never recommend.....as long as system can deliver appropriate air flow with a pleated cotton filter...and any decent service tech can check the air flow for proper cfm]. Any particles small enough to pass through a pleated cotton filter are going to pass through a second filter as well....unless the second filters are so tight that the system is starving for air flow. Has anybody ever accidentally put two filters in their automatic drip coffee maker? What if cars used two fuel filters or air filters? I have told some homeowners to try using second filters at each register [the black thin filter material cut-to-fit....same type used in many window air conditioners].....but I only suggest this when I know they will still get at least 400 cfm per ton of air flow [350 absolute minimum]......as some homeowners know others who say it has helped and it gives them a peace of mind knowing they are doing something to help contribute to a solution, so it HAS to help [even though I think it falls in the "one-born-every-minute" category.....similar to duct cleaning].
My 48 yr old house (mine for the last 4 yrs) has considerable dust in the return plenum (fiber duct). I’m remodeling and recently re-sealed the return plenum AND the site-fabbed transition built when the new unit was installed, 2013. The return was leaky no doubt drawing musty, dusty air from the crawl space due to the Red-Neck fab & seal job! Pitiful craftsmanship! It took me 7 hours to fix the new transition piece. Anyway, the dust in the house is the same “color” as whats in the return duct and I’m getting way too much & too often in the house. I’ve also cleaned my coils, which were not that dirty.

I was told that 15 out vents would be cleaned and one main vent. the guy came over and gave me an estimate of $500. I had acquired a groupon for $49. the guy said just doing the out vents and one main vent would accomplish nothing. Now I am in dispute with the groupon people for a refund which they won’t give and have to go ahead and waste the money and let them do it. Is their doing the 15 outvents and one main one going to accomplish anything?
Had our ducts cleaned late April, 2016. Sodium Chlorite was sprayed into ducts after cleaning. Ever since, we have been bothered with eye and nasal passage irritation because of a “chemical” and “musty” odor. This odor is present whether or not a/c is on.) We are told the sodium chlorite (“EnviroCon, manufactured by Bio-Cide International) is used in hospital and nursing home settings and is not hazardous to health. The air duct company’s suggestion is that they come out and spray even more sodium chlorite…we absolutely don’t want this done! Have had various other recommendations about what we need to have done to remedy our problem. We will be unable to stay in our home if a resolution cannot be found. We’d be willing to replace the ductwork if necessary. (One professional suggested that the cleaning may have “knocked something loose” inside the ductwork and that is the source of the irritant.) This home was built in 1920…no idea when the present ductwork was installed. Any suggestions would be appreciated.
Concealed behind your walls and mostly ignored, your air ducts serve as vital pathways that deliver warm and cool air throughout your home. While they may be unseen, your air ducts are working whenever you have your air conditioner or furnace running–nearly year round. Attached to your HVAC, air ducts transfer the air from these systems throughout your home. What many homeowners don't realize is that your air ducts, in nearly constant use, continually accumulate dust, grime, debris, pet dander, and allergens throughout the year. A professional air duct cleaning is necessary for better indoor air quality and the health of your family.
In addition, the black dust was found in most of the heat registers. He could rub it off on his fingers but did nothing but spray compressed air on it which didn’t make it disappear since it wasn’t loose. Also, in the register in the basement he described the black dust as being oily. The reality of that situation is that I had the AC on until the morning of the service and minutes after he snaked the hoses in my back door it started raining. The basement register had condensation from the humidity all over it. It was not oily but wet. He asked for an old towel and wiped it out. Never saw anything so black – because I never had to clean soot. That is what I have in my ducts. Soot from years of the old coal furnace.

If no one in your household suffers from allergies or unexplained symptoms or illnesses and if, after a visual inspection of the inside of the ducts, you see no indication that your air ducts are contaminated with large deposits of dust or mold (no musty odor or visible mold growth), having your air ducts cleaned is probably unnecessary. It is normal for the return registers to get dusty as dust-laden air is pulled through the grate. This does not indicate that your air ducts are contaminated with heavy deposits of dust or debris; the registers can be easily vacuumed or removed and cleaned.

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