i just recently got a Fender MIM Stratocaster with vintage tremolo and i was just playing. I was about to go tune it up and went to go do a natural harmonic on the 5th and nothing happened noise.All of the other frets that natural harmonic happen on worked except the fifth.Does anybody know what making this happen and how i can fix it?

hmmm.... looks like u got a dead fret(s) id get that checked out... my santana 2 had a dead fret but on the 17th fret or sumthin and the prob is the string is too close or too far from the board it was fixed with a simple raising of the bridge =) gl tho.
btw i think u can check it by getting a piece of metal and laying it exactly on the top of the fret and playing the note if it makes a sound different from the other harmonic frets (7th, 12th etc.) then get it checked
Having a dead fret would not affect harmonics, intonation would though.
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