Examine the framing of the roof with a flashlight. Look for drops of water or water stains. It is best to do this after a rainstorm or when snow on top of the roof begins to melt. On a sunny day, look for spots where sunlight is shining through the nail hole.
Caulk all nail hole leaks with roofing cement. Apply the roofing cement with a putty knife around the damaged area inside the attic. For extra security, inspect the shingle on top of the roof and apply more roofing cement to the top of the nail.
Cover the hole with sheet metal. This is an alternative method for repairing nail holes. Tuck a piece of sheet metal under the shingle with the hole in it. Sheet metal comes in flat pieces and coiled strips. The top piece of the metal should be about an inch up the slope from the hole. Use urethane caulk to secure the sheet metal in place. Urethane caulk has a low shrinkage factor and is water-resistant. Apply the caulk with a caulk gun. Wipe off excess caulk with a damp rag.
Inspect the roof twice a year. Replace shingles that have holes that are too large to patch. Always use roofing cement to cover the nail heads after nailing shingles in place.