http://img209.imageshack.us/img209/8892/kassadinmh.jpg

First things first. Props to killraven and his build "Kassadin: Badass Rift Ninja"
If you are new to Kassadin I recommend starting with his build. This will allow you to learn when you can engage and still make it out to fight again. Once you feel you are having no problem with Kassadin move onto this one :D

*However I still recommend using

The only things you are worried about within the masteries for Kassadin is the damage of your R-Q-E combo and how many times you can do it without running out of mana.

This is the purpose of taking Archaic Knowledge in Offense, and every Mana regen point in Utility.

Normally in mid you are going to be against a squishy--and because of this the tome gives you that extra burst on each attack. You will have endless, high-damage attacks due to this with your early game clarity. This will allow you many opportunities to get a kill within the first 3 levels.
Normally by the time you get that first kill you will be buying this flat out for the 1100. You need this extra movement. The MPen is just a great addition.

Depending on who you are against in mid you want to be buying constant, do NOT underestimate the effect these have early-game with a low HP champion such as Kassadin. Everytime you R-Q-E combo you will take down a midding mage to about 50% or less. You will be left with about 50-80% depending. These HP pots allow you to do one R-Q-E combo for each 1 or 2 potions.
All of this harrassment will land you enough money for your Mejai's. From this point on you do not want to die. This doesn't mean stop using R offensively. This is the reason you have. You now have a secondary escape. If you are out ofby now, BUY MORE. 2-3 At all times if possible. This is also where you want to start ganking the lanes. Kassadin is slow at pushing a lane so make sure you've either killed the opponent or pushed the lane up far before you leave mid.
With theyou've grown to become addicted to, you'll spend a lot of time in mid instead of at base. After a couple levels and 2-3 kills you will have enough for your NLRod. This extra 80 AP on top of your 6~8 Mejai Stacks should be enough to take any non-tank champion down to atleast 20% in one combo if not completely.Same as above, though I prefer waiting for the NLR usually.
You should be at 400AP now normally at around lvl 11-13.
THIS is the badboy that makes the difference of a 13-10 game and a 13-0 game. If you are stacking Mejai's and planning on keeping 20 stacks there is no reason not to make a leviathan. 820 HP + 15% LESS damage taken from champions at 20 stacks. Every game that I play with Kassadin I reach 20 stacks on this item. Once you do, you can enter into those 1v3 battles, kill 1 or 2 and R out of there.
This will give you that extra mana boost/regen to allow you to R almost as many times as you please with adding in clarity. I normally like to buildfirst as you will be max Mejai stacks by now and won't want to base. You will build up that extra mana.
More AP and more survivability. You can have more HP than your tank at this point and still hit like a truck with your 900ish AP and 3600 HP.

You ALWAYS want to mid with Kassadin on this build. The key to staying ahead in mid is to stand in between your opponent and his minions. Kassadin is scary to mid against if you do not have a stun. This will withhold plenty of EXP from your opponent. Once you hit 6 just R-Q-E-R-Q.

Any questions? :D