MAGIC RESISTANCE is the chance a spell might fail when cast on the monster; this chance is expressed in a percentage. The basis for the percentage is a spell cast by a magic-user of the 11th experience level. If player character spell casters are not of the 11th level, the figure must be adjusted upwards by 5% for each level below 11th, or downwards by 5% for each level above 11th. Thus, a monster with 95% magic resistance cannot be affected by a spell cast by a magic-user of the 10th experience level or lower, while a 12th level magic-user has a 10% chance of affecting it.
Note that even if a spell does overcome the magic resistance of a monster, the monster is still entitled to normal saving throws. A creature's magic resistance extends only to its immediate possessions, i.e., anything carried or worn. Area-effect spells will still function if targeted on a magic-resistant creature within their area. The creature itself might not be affected, although all others in the spell area will be subject to spell effects. A fireball, for example, may wipe out a cluster of orcs, while an agathion standing in their midst might be totally unaffected.
The percent of magic resistance of a creature has an effect on certain existing spells such as hold portal, where it indicates the probability of shattering the existing spell.
—Monster Manual II.