I still consider myself a beginner, I have a mexican strat that I purchased about a year ago.. Lately it seems like i can have all my strings in tune but as soon as i start playing the third string from the bottom sounds flat and the rest sound wonderful. According to my tuner they are all correct.
Could there be something that is causing that one string to sound flat?

Most probably the guitar's intonation.

Basically due to scale length + tension + thickness of strings everthing can be perfectly intune in the open string position, but as soon as you start moving up the neck things can start going out of tune.

To fix this, set the intonation properly. You'll need a phillips head screwdriver. Check out this vid for details.

http://www.youtube.com/watch?v=GZVRCMJLnm4

If you're uncomfortable setting up your guitar like this yourself, take it to a shop to get it setup properly.

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My Rig: Guitar into Pedals then into Amps and out into Speakers.

You said you got the guitar a year ago, when is the last time you changed the strings?

Yeah sounds like an intonation problem. Get your Strat set up properly. Check this out:
http://www.fender.com/support/stratocas ... _guide.php

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Obligatory gear list: Fender, Rickenbacker, Gibson, Gretsch, Vox, Martin, and more Fender.

atolleter, I have never replaced the strings, they are the ones that came on it. How often do they need replacing?

That means that the strings are at least a year old. The string you speak of is the G string, this one usually takes the most bending of the six. Since it seems you have not changed anything in your setup the string may very well just have lost its elasticity over time. Before you mess with any settings, do yourself a favor and buy new strings, make sure they are the same gauge as these.

thanks for all of your responses, i will check on changing my strings and let you know, thanks again

Yes, post back after you replace so we know that you're all set.

I would get new strings and if you havent had it set up ,I would do that too.If you play alot I recommend changing strings at least once every 2 months.I usually end up changing mine every month at least.

I change my strings quite often. I would guess no more than around 25 hours of playing time on them. that's for playing around home.

When i used to play out, if i was feeling like a daredevil sometimes i would risk 2 shows on one set of strings, but usually I would make sure the main guitar had a fresh set before every show. (Guess how much fun breaking strings on stage because they're old is.)

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I'm not an expert, but I play one on the internet.

I change my strings at least once a month,when I was gigging I changed every week.Dwarren as others suggested a string change should certainly help,if not,consider getting a complete set up usually less than $100 and well worth the expense.With a complete set up they set the intonation,adjust the string height/action and adjust the truss rod but make sure that the person doing it is qualified.To prolong string life in future wipe the strings thoroughly after playing and make sure that your hands are clean before playing.One year is far too long to let a guitar go without a string change even if the guitar wasn't played as the strings would most likely stretch and corrode somewhat.

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'65 Strat,65 Mustang,65 Jaguar,4 more Strats,3 vintage Vox guitars,5 Vox amps,'69 Bassman with a '68 2-15 Bassman cab,36 guitars total-15asst'd amps total,2 vintage '60s Hammond organs & a myriad of effects-with a few rare vintage ones.

thanks for everyone's help and suggestions, I decided to take my guitar in to the fender dealer where I bought it, I found out they will restring and set up and clean it as long as I own it for free, all I had to pay for was the strings. It sounds wonderful once again.