A skylight can be installed on just about any roof regardless of the slope or roof covering. But it must be the proper skylight for the application. The use of the wrong type skylight increases the potential for problems.

Flashings will tend to lift and separate with age as membranes dry out or become distorted with thermal movement or settlement of the structure. Periodic resealing and repair of the flashings is a standard maintenance requirement. In some cases skylight joints, seams, and flashings are coated during installation as a precautionary measure. However, a good quality/properly installed skylight does not rely on cements and sealant to prevent leakage. The existence of surface sealants may be an indication of leakage.

Skylights are subject to damage from falling tree branches and other debris. Poor quality plastic glazing can break down or become discolored from the ultraviolet rays of the sun. Heat can also distort the glazing. Surfaces can be scratched from squirrels and other pests. Fortunately, aside from broken glazing, these conditions do not necessarily cause leakage.

To minimize injury from glass breakage, safety glass or plastic should be used in skylights. Labeling in a corner of the glazing may provide confirmation that it is safety glass. However, requirements for safety glazing are relatively new; older skylight units may have been manufactured prior to the establishment of current standards. Many newer units are plastic, especially if they are curved shapes such as dome or convex units.

Ideally the skylight should be installed on raised curbing which lifts the skylight above the roof surface and facilitates the installation of flashing or manufacturer-supplied trim to make it watertight.  Installing a diverter at the topside of the opening helps to divert the roof runoff away from critical joints. Flush-mounted skylights or skylights with relatively low curbs are especially susceptible to leakage.

Like windows, skylights form a minimal barrier between the warm, moisture-laden air on the living space side and the frequently colder environment outdoors during winter months. This temperature differential can lead to the formation of condensation on the inside surfaces. The amount of moisture caused by condensation can be substantial enough to cause staining of adjacent ceiling surfaces and appear to be leakage. Maintaining proper temperature levels and air exchanges (using ventilators) within the house will help keep indoor moisture levels at a reasonable point. The use of double glazed units may also help control condensation, as well as reduce the amount of heat loss.

The loss of heat through a skylight can contribute to the formation of an ice dam, usually below or down slope of the skylight. See the Homeowner Information Series on Ice Dams for more information.

Double-glazed skylight units are subject to failure from manufacturing defects, installation deficiencies, warping of the frame, damaged sealants and other factors. These failures are difficult to detect in many cases, as certain climatic conditions must be present. Eventually the seal failure may manifest itself as condensation within the window, fogging or discoloration of the glazing. When this occurs, the amount of light transmission may be affected but the difference in heat loss may not be significant.

Under direct sun some skylights can produce "hot spots" on interior surfaces. This can result in discoloration of the carpeting and other finishes from the ultraviolet rays of the sun. Shades are recommended.

All skylights should be periodically inspected by qualified individuals for the presence of damage or other conditions that can cause or contribute to leakage and other detrimental situations. More specifically, all flashings, glazing, and related components should be checked for lifting, separation, and other damage.