Determine whether the pet odors are due to urine in the ducts. Check any floor vents your pets may have access to and shine a black light around the vent and into the duct. Urine stains will glow under the black light. If urine stains are present, clean the area around the vent with a pet urine cleaner (available in pet stores), or a solution of 1 part vinegar and 1 part baking soda. This prevents the animal from continuing to urinate in the vent.
Hire a professional air duct cleaning service to come into your home and clean out your duct work. Professional air duct cleaners use special tools such as vacuums, blowers and brushes designed specifically to clear out pet dander and debris (as well as other dust and debris) from your duct work. This eliminates odors in the the ducts as well as helping reduce colds, coughing and allergies due to inhaled pollutants.
Consider using a product designed for eliminating air duct odors, which you spray into the ducts and allow to work its way into the system, freshening as it goes. These types of products treat odor problems by destroying odor-causing bacteria, covering odors with a more pleasant smell, or actually removing odor particles that have become stuck in the ducts.
Maintain the cleaned ducts by regularly cleaning the area around the vents to prevent build-up of pet debris as well as to prevent pets from using the vents as a bathroom. Also, have a yearly duct cleaning by professional cleaners to maintain your cleaned air ducts and prevent pet odors from accumulating.