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In D&D 3.5 you don't get skill points retroactively, only from the next level onwards after you increase your intelligence enough to gain an increased bonus, leading to extra skill points per level.

However when playing today a friend of mine mentioned that Pathfinder is different, and that skill points are applied retroactively when your intelligence bonus increases. But I can't find anything in the rule book that mentions which it is either way.

Can someone please clarify for me which it is and point out where it is stated?

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Yes, you do.

Read in the Ability Scores section of the SRD, or Core Rule Book p.554, Appendix 1: Special Abilities:

Permanent Bonuses: Ability bonuses with a duration greater than 1 day actually increase the relevant ability score after 24 hours. Modify all skills and statistics as appropriate. This might cause you to gain skill points, hit points, and other bonuses. These bonuses should be noted separately in case they are removed.

In specific reference to this being a change from 3.5, James Jacobs notes on the Paizo boards that

All bonuses are retroactive when an ability score increases, be they bonuses to damage, to skill ranks, to hit points, to saves, to skill checks... all of them. Skill ranks not being retroactive are a 3.5 convention we specifically removed from the game because it was a weird exception to the rule, and since now there are no exceptions to this rule, there's no need to specifically state that skill ranks are retroactively granted if your Intelligence goes up.

There seem to be a lot of Pathfinder questions lately that fail to understand the general principle that unless there's a specific exception noted, yes, everything happens according to the general rule even if it's not listed out specifically. This is a case of that.

The most prominent exception is the Headband of Vast Intelligence, which gives you extra skill points but locks them to one specific skill and doesn't let you choose. However this is NOT to be generalized to other items; for example the robe of runes and some intelligence-boosting ioun stones do not explicitly bear this restriction and therefore would give you skill points as normal. It's tricky though, because even other similar intelligence-boosting ioun stones do have that same restriction! An item follows the general rule of giving back skill points unless it has a clause saying it doesn't. And if it doesn't, make sure and note what you spend those skill points on in case you lose them.

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