Vacuums by their nature cause dust to become airborne, by exhausting air that is not completely filtered. This can cause health problems since the operator ends up inhaling respirable dust, which is also redeposited into the area being cleaned. There are several methods manufacturers use to control this problem, some of which may be combined together in a single appliance. Typically a filter is positioned so that the incoming air passes through it before it reaches the motor, and then the filtered air passes through the motor for cooling purposes. Some other designs use a completely separate air intake for cooling.

It is nearly impossible for a practical air filter to completely remove all ultrafine particles from a dirt-laden airstream. An ultra-efficient air filter will immediately clog up and become ineffective during everyday use, and practical filters are a compromise between filtering effectiveness and restriction of airflow. One way to sidestep this problem is to exhaust partially filtered air to the outdoors, which is a design feature of some central vacuum systems. Specially engineered portable vacuums may also utilize this design, but are more awkward to set up and use, requiring temporary installation of a separate exhaust hose to an exterior window.

--Bag: The most common method to capture the debris vacuumed up involves a paper or fabric bag that allows air to pass through, but attempts to trap most of the dust and debris. The bag may be disposable, or designed to be cleaned and re-used.

--Bagless: In non-cyclonic bagless models, the role of the bag is taken by a removable container and a reusable filter, equivalent to a reusable fabric bag.

--Cyclonic separation: A vacuum cleaner employing this method is also bagless. It causes intake air to be cycled or spun so fast that most of the dust is forced out of the air and falls into a collection bin. The operation is similar to that of a centrifuge.

--Water filtration: First seen commercially in the 1920s in the form of the Newcombe Separator (later to become the Rexair Rainbow), a water filtration vacuum cleaner uses a water bath as a filter. It forces the dirt-laden intake air to pass through water before it is exhausted, so that wet dust cannot become airborne. The water trap filtration and low speed may also allow the user to use the machine as a stand-alone air purifier and humidifier unit. The dirty water must be dumped out and the appliance must be cleaned after each use, to avoid growth of bacteria and mold, causing unpleasant odors.

--Ultra fine air filter: Also called HEPA filtered, this method is used as a secondary filter after the air has passed through the rest of the machine. It is meant to remove any remaining dust that could harm the operator. Some vacuum cleaners also use an activated charcoal filter to remove odors.

Ordinary vacuum cleaners should never be used to clean up asbestos fibers, even if fitted with a HEPA filter. Specially-designed machines are required to safely clean up asbestos