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The term roof penetrations refers to an apparatus that juts out from the roof. The most common of these are vents. Vents are necessary for plumbing, exhaust fans, to release hot air from the attic and to channel combustion gasses from the furnace and wood stove. You'll even sometimes see dryer vents on the roof.
Anything that breaks the seal of the roof can lead to possible water leaks and the resultant mold, mildew and/or water damage. A poorly-designed combustion vent can also lead to condensation problems, leading to water under the roof line. The most common problem with roof penetrations is improperly-installed flashing around the openings. Without flashing to lead rainwater and melting snow away from the sides of the vent, water can -- and will -- enter the house. On flat roofs, roof penetrations require a curb around them, that is a raised platform, to help deflect water away from the penetrations.