Unless you have some acute illness I would not worry about the ductwork. A recent study stated that cleaning home ductwork was really not necessary since the dust and dirt in the duct work, once settled, tends to remain in the ductwork and does not travel through the furnace. You furnace filter catches the airborne particles that have not had time to settle. It did recommend removing the grills and vacuum around the openings to remov the spiderwebs and loose particles that tend to settle and move onward.
There are companies, listed in the phone directory, who specialize in this process. It really cannot be done by the homeowner since it requires special equipment.

My wife has bad allergies, and we recently bought a 45-year-old home that was canine and feline central for most of its time. We had the ducts professionally cleaned, and it did make a world of difference in the way the house smelled, and my wife has not had any problems with it. Of course, we have no previous experiences in the home, so it doesn’t really prove anything.

The research we have done on the matter basically agrees with DrHome, with a few additions. For one, having the ducts cleaned out after the house is built (or remodeled) will reduce the initial debris being blown about the home, but gradually, everything that can blow around the home will, and the heavier stuff won’t.

After that, it seems to be a good idea to clean out the ducts when you buy a used home, like in our situation. As you live in your home, it becomes full of your family’s germs, skin particles, etc., etc., but that’s okay because you become sort of immune to your environment, or at least tolerant. When you buy someone else’s home, you inherit, for at least a short time, some other family’s germ pool. Cleaning things like ducts and carpet go along way to help with that transition.

Beyond that, the articles seem to be somewhat divided on regular cleaning. I tend to agree with DrHome and those articles that do not believe additional cleaning is necessary. But to make sure you understand all points, the side that recommends a regular cleaning (3-5 years) do so because they believe germs and viruses can manifest themselves and thrive in ductwork full of particles of debris, particularly in a warm, moist environment like what can be found in forced air heat with a whole-house humidifier.

For the record, I removed the whole-house humidifier in favor of room versions. We are also looking at various filtration units for our heater since studies we have read show a dramatic improvement in air quality. At $300, the unit we are considering is only $25 more than the ductwork cleaning service.