Dall'SRD:
When a creature has more than one natural weapon, one of them (or sometimes a pair or set of them) is the primary weapon. All the creature’s remaining natural weapons are secondary.
The primary weapon is given in the creature’s Attack entry, and the primary weapon or weapons is given first in the creature’s Full Attack entry. A creature’s primary natural weapon is its most effective natural attack, usually by virtue of the creature’s physiology, training, or innate talent with the weapon. An attack with a primary natural weapon uses the creature’s full attack bonus. Attacks with secondary natural weapons are less effective and are made with a –5 penalty on the attack roll, no matter how many there are. (Creatures with the Multiattack feat take only a –2 penalty on secondary attacks.) This penalty applies even when the creature makes a single attack with the secondary weapon as part of the attack action or as an attack of opportunity.
Dalle FAQ:
A secondary natural weapon is always a secondary natural
weapon, even when a creature attacks only with that weapon. A
lizardfolk attacking with only a bite has a –5 attack penalty (–2
with the Multiattack feat) and gains only 1/2 its Strength bonus
with the bite attack. Secondary weapons are inherently less
effective than a creature’s primary natural weaponry, mostly
due to limits of the creature’s fighting skills or physiology.