Penetrations and Flashing

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Checking that Penetrations and Flashing are Installed Correctly

Improper flashing or pipe boot installation is over (half) ½ of all the roof leaks Litespeed Construction repairs. A Pipe Boot is classified as a penetration, which is any exhaust vent opening in your roof. The flashing is the seal that is used around a penetration to keep water out of it. It is critical that penetrations and flashing areas be installed correctly to avoid a higher risk of leaks from occurring.

To dive deeper into penetrations and flashings we will examine the following areas:

  1. Correctly flashing Pipe Boot penetration areas and common failures
  2. Flashing Applications
  3. Incorrect flashing

1. Correctly Flashing Pipe Boot Penetration Areas and Common Failures

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Lead Boot: Incorrect Flashing – Nails not sealed

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Lead Boot: Correct Flashing

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Improper Pipe Boot Installation: Over Shingles

So here are a few tips on how to properly install flashing around penetrations and walls:

  1. Use high quality material for pipe boot penetrations and for flashing metals.  The International Residential Code (IRC) actually describes the weight of steel and aluminum to be used for flashing.  Aluminum, plastic and silicone boots are all acceptable materials.
  2. Nail and affix your flashing correctly to the roof and walls.  Meaning cover nails with shingles and paper as necessary. Leaving exposed nails provides opportunity for water to go in those nail openings and cause leaks.
  3. Make gravity your friend.  Always lap materials where gravity sheds the water, not the other way around.
  4. Use Ice and Water Shield at all penetrations and flashing on your roofs. Visit our Ice and Water Shield page for more information on this (make this a clickable link to this page). However, in short Ice and Water Shield seals around nails that are put thru it, and causes a very tight seal around the nail.
  5. Never build or install your home with penetrations that are within 3 feet of valleys or pitch breaks, where at all possible as these areas have the highest concentration of water flowing thru them.  

Penetrations have a multitude of ways they can be done incorrectly. Here are some of the most common misinstallation problems:

  1. Unsealed nails at Pipe Boots. In the pictures above you can see that sometimes a Pipe Boot by default lands low enough down on a shingle row that the shingle does not completely cover the whole base of the boot. That is acceptable, but only if the nails holding it in place are then sealed off. If they are not it leaves an opening for water to travel into. However, if a nail is covered by a shingle sealing is not necessary.
  2. Placing nails in the wrong areas is also an issue. Pipe Boots have indents in the base that nails are supposed to go into. This is to help assure that nails are not placed too close to the edge. Placing nails too close to the edge compromises the edge and encourages water to flow in around the edges.
  3. Placing Pipe Boots down before putting the shingles on is another mistake. Sometimes contractors think this is good because the nails are then covered by the shingles completely. However, the Pipe Boot is meant to sit between the layers of the roof. If shingles are positioned on all sides of the boot it encourages water to run down the Pipe Boot to the base and collect under the shingles.
  4. The other issue to consider is using an incorrect Pipe Boot size. This one’s self explanatory, but when a Pipe Boot does not fit the opening correctly it leaves openings for water to come in.

Another issue for Pipe Boots that don’t work well is Pipe Boots that perhaps were installed correctly but end up failing in time. The downside to Penetrations such as Pipe Boots is that they are not typically designed to last as long as the life of a roof. Sometimes people attempt to seal around them to make them go longer, but these glues are not made to last either. The average roof has plastic Pipe Boots on it. Plastic degrades over time due to weather, especially in direct sun. Overtime the plastic will dry rot and become brittle and crack. The best solution to this is to purchase an upgraded Pipe Boot such as a “Lifetime” brand Pipe Boots. Visit here for more information on “Lifetime” boots. The differences with these boots is that they are made of silicone instead of plastic allowing for a longer life span.

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“Lifetime” Pipe Boot

2. Flashing Applications

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Installing Step Flashing

Step flashing can be and should be used on any part of the roof where a vertical wall meets a slope. Flashing is made of metal and  prevents water run off from going under the shingles and damaging the roof decking. This means the most essential places to have flashing is where water would have the strongest downflow onto another portion of the roof. There are several different types of flashing depending on the area they are being used in. Step flashing for example is an “L” shaped metal usually made from aluminum that is fastened to the wall on one side and placed under the shingles on the roof side. The counter flashing goes on top of the shingles and over the Step flashing and can also be called Cap or Cover flashing. It is also metal but more typically made from copper, galvanized steel, tin, aluminum or even sometimes plastic.

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Proper Counter Flashing

There are three main ways to mount Counter flashing. The first is through-wall flashing, which is really only realistic on new builds. The second and often more realistic method to accomplish is surfacing mounting. It is critical that surface mounting be done correctly, if not water can leak in between the cracks. This is prevented by caulking the seams to make a tight seal. Done correctly this can last a long while, however degradation of the caulk is still possible, so it is recommended to monitor the caulk for any signs that it might need touch ups. The last method between these two is the reglet method. With this method a groove is cut out of the wall so as to insert the flashing more into the wall and prevent water penetrable gaps. This version tends to be very water tight.

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Through-Wall flashing

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Surface Mounting

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Reglet Flashing

In short, standard flashing is a two part mechanism consisting of Step and Counter flashing. Step is almost always covered by a wall material like stucco or vinyl siding or hardie or some other counter flashing mechanism such as Counter flashing.

3. Incorrect Flashing

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Incorrect flashing installed above the shingles

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Step flashing only no Counter flashing

Putting flashing in the wrong place or omitting necessary flashing are both mistakes that are important to avoid. But even other small issues such as nailing inconsistencies can be just as critical to preventing a leak.


When referring to putting flashing in incorrect places a big mistake is installing flashing over the shingles instead of under them. If flashing is put over the shingles there is nothing stopping the water from running under the flashing and going between the shingles.


Another issue is putting Step flashing down but forgetting the protective Counter flashing over top. Step flashing is not meant to be exposed and needs to be covered by something, whether it be further flashing or another material like stucco or siding. This helps to ensure a proper full shield against water flowing in.

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While both of these previously mentioned issues are rather large and easy to spot some issues are more subtle. Sometimes contractors put the counter flashing over the step flashing like they are supposed to but they do not overlap them in the correct spot. Or they place the flashing in the right spot but they put nails in an incorrect location causing leaks to form. has a terrific article mentioned this point.  3 of the first 5 roof leak mentions are directly related to improper flashing in this article opinion.