Basically this build of Mordekaiser focuses on making him a tanky AP champion.

The runes are a combination of Magic Penetration, Health Regeneration, and Magic Resist. The magic penetration is good for early game kills, farming (which is something Mordekaiser is VERY good at), and obviously for a better harass. Plenty of Health regeneration is good for Mordekaiser, since his abilities cost health to perform. It also allows Mordekaiser to stay in lane longer without having to return to the base often which bring a lot of benefits in general, i.e. more gold, faster lvl ups, etc. And finally the Magic Resist. Often times you will be laning against other magic based characters, and this really helps a lot especially if you are laning against say Annie, or Brand who are both magic based potential nukes. Use 9 of each and support your three types of runes with a quintessence. This should maximise the effects of your runes.

For Mordekaiser's masteries you might think a strong defence is preffered, however the opposite is the case for him. Having strong Utilities allows mordekaiser to perform most efficiently while laning and farming, also in kills and harassing. The utility mastery set also give a bonus to your ghost spell. By nature, Mordekaiser has a strong defensive shield, so we can simply support our abilites to work in unison with our runes, such as the magic penetration. The nine points in offence are a good way to reinforce your magic penetration, ability cooldown, ability power and reinforces our summoner spell (exhaust). I dont reccomend feeding your defensive mastery set for mordekaiser, simply because he is a much more potent advisary when he is delivering maximum damage. The items grant a lot of bonus for defence as well.

1. First of all buy a regrowth. Your health regeneration will be about 25 HP/5 Seconds as son as the match starts. This means lots of time to sit and farm/lvl up.
2. Sorcerers shoes next, this is obvious.
3. The giants belt adds quite a bit of health, and beefs up mordekaiser even more. Since it doesnt cost a lot you could potentially have all three items in less than 10 minutes(if you get 1-2 kills or assists)
4. Warmogs is preffered for a boost in health regen, and makes Mordekaiser even more intimidating to see, i.e approx-2400 hp along with a full shield approx 2-400 extra HP by lvl 8.
5. Negatron CLoak to enhance your magic penetration.
6. Force of nature grants a huge bonus to your HP regen. Which should be @ about 60-70 HP regen/5 seconds.
7. Another giants belt, or if you have the cash, buy a Ryalis. Ryalis is next for the slowing effects. Makes your Siphon slow, gives even more HP and adds a boost to your AP.
8. The next item to buy is an Abyssal. This is a great choice for some more AP, a giant boost to your Magic resist, and lowers enemies Magic resistance ( huge difference is noticed due to your already over powered Magic Penetration.
9. The last item is just for jokes by now. You could potentially buy this one ealier but i usually wait till late game for this because it is more or less just giving even more boosts to the magic penetration and ability power.

Max out siphon of destruction as early and fast as possible. I like to use the siphon of destruction and mace of spades combination for farming and shield building. Creeping death is more of a defensive ability, which does help early game, but i usually wait until lvl 3 to get. The lvls go by pretty quickly when you are farming lanes with your abilities and magic penetration.

LANING COMBO:
1. SIPHON OF DESTRUCTION,
2. CREEPING DEATH,
3. MACE OF SPADES,
4. SIPHON OF DESTRUCTION,
5. MACE OF SPADES,

FIGHTING ENEMY CHAMP COMBO:
1. SIPHON OF DESTRUCTION,
2. CREEPING DEATH,
3. MACE OF SPADES,
4. SIPHON OF DESTRUCTION,
5. SPELL (EXHAUST)
6. SPELL (IGNITE)
7. MACE OF SPADES
8. CHILDREN OF THE GRAVE
---if the enemy is still alive---
9. SIPHON OF DESTRUCTION

EXHAUST: Tired of chasing those pesky runners? Exhaust them before they can go. This spell is quite useful against heavy AD carrys, or DPS champs who kill in four or five shots. It allows you to use a few extra abilites and chase the enemy down using Creeping Death.

IGNITE: What Mordekaiser is complete without his classic IGNITE+CHILDREN OF THE GRAVE combo? None, thats who. :P