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Whats the rules/restrictions for using allies in a 40k game?

272-273 of the main rules is as close as it gets - outside of Apocalypse.

Which is to say, there is a specific mission with some rules to cover it.

Editing to add:
Those only half cover it even, pretty much the idea being that the armies are not the same so they cannot share rules - i.e. Even allied Tyranids do not share Synapse.

So its not a common thing to do then?

Not really.

Happens often enough in campaign play, and things of that nature, but those tend to have a fair number of house rules and exceptions.

Alright then, thanks kirsanth. I was just wondering if there was a general rule like adaptations with the force organisational charts or something. Thanks for clearing it up!

Sometimes we have played with multiple people sharing a FO chart - almost every time we also use a single codex and share rules. (Despite what I just wrote. This is a lot less common though).

Mostly it is important to keep the armies separate so that you do not have Space Wolves using Vulkan's rules for making master-crafted thunderhammers, and other such silliness.

All that said, there is not reason not to do what you find fun, especially once you start playing by your own rules.

Editing to add:
Another member, Reece, is holding a tourney with team rules:
http://www.frontlinegaming.org/community/bay-area-open/warhammer-40000-team-tournament/

More information is in the tournament forum, near the top atm.

Fair enough, the reason I ask is because a while ago I ran an IG army (legal with HQ and troops etc) with an allied inquisitor +henchman unit. The fluff behind this is that the inquisitor had requisitioned the IG company to aid him in his investigations etc and I wondered if this would be legal just to play other than friendlies. Link useful cheers!

Ah! There were rules for allies regarding the Inquisition, but I do not believe any are still currently 'legal'.

Ah I see, that's a shame.