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I have a skylight on a shingles roof. I don't know much about the skylight as it was installed by a previous owner, but every year, at the beginning of the rainy season, the skylight leaks. And every year, when that happens, I go on the roof to add some sealant, which usually gets me through the rainy season.

In the first picture below (click to enlarge), you can see the skylight, the shingles, and the sealant. The second picture zooms on the sealant, which starts cracking. Finally, the 3rd picture shows the sealant I used. I am thinking that the sealant cracks during the summer, explaining the leak when we get our first good rain of the year.

What would you recommend to fix this problem in a more permanent way?

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While Flashing is the most important step, and therefore this is NOT an answer, I've found that the DAP roofing sealant is... and DAP products in general are... utter crap. I would recommend instead the Blackjack #21 (we nicknamed it "blackhack") elastomeric roofing sealant and patch, with 2nd choice being the Henry #209. –  Karl Katzke Sep 20 '11 at 18:04
    
When you finish gooping it, collect some shingle gravels from the gutter and put them on top of the goop. Make it look like the shingles. This will slow the UV rays from degrading your goop, as it does the shingles. If you have a lot of gravel in the gutter, you probably need a new roof. –  Randy Aug 18 '13 at 14:23
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2 Answers

A skylight (and any hole in the roof) needs flashing, not caulk. The flashing should be overlapped so that shingles above are on top of the flashing, and as it goes down the side, each piece is on top of the piece below, so that any water runs down the roof rather than in your home. The flashing should go up the side and under any lip from the top of the skylight so that rain from above cannot get in behind the flashing. And then all nails should be covered in a roofing caulk and under a shingle/above flashing/other protective layer.

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That looks like a Solatube or similar product. (Home Depot sells ones made by VELUX, a skylight company.) You should be able to ind flashing for it, and like BMitch has said, flashing is pretty darn important. If it's a Solatube, here are some links to their flashings: http://www.solatube.com/commercial/product-catalog/brighten-up-series/index.php , http://www.solatube.com/commercial/product-catalog/solamaster-series/index.php . If it's another brand, I'm sure flashings exist... you'll just have to look for them.

I would also recommend using a different sealant. Polyurethane or nitrile rubber (not going to find it at Home Depot or Lowes, but it's good too.)

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+1 I was actually scratching my head on the round skylight. Thanks for the added details! –  BMitch Sep 20 '11 at 14:29
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