Two main places on your toilet might give you stuck toilet bolts: the base and the tank. The most common place for stuck toilet bolts is at the base. Normally, two plastic caps cover the bolts here and keep them dry. These caps, however, can fall off or get knocked off, leaving the bolts exposed to the damp environment of the bathroom, which will eventually lead to rust. A number of options will help you remove stuck toilet bolts.
Remove the plastic bolt caps over the bolts by inserting the edge of a flat-blade screwdriver or sharp knife underneath the caps and popping them off.
Brush off the bolts with a stiff wire brush to remove any rust or build-up.
Spray penetrating lubricant on the stuck toilet bolt. Allow it time to soak in according to the manufacturer's instructions. Unscrew the bolt with a wrench.
Heat the stuck bolt with a propane torch instead of applying lubricant. This expands the bolt and may make it easier to remove. Unscrew with the wrench.
Slip the end of a nut splitter over the toilet nut as another alternative to removing the bolt. Tighten the end clamp hand-tight. Turn with a wrench to drive the point of the splitter into the toilet nut. The splitter should cut the nut in half, leaving the bolt free.
Saw off the nut portion of the bolt with a hacksaw instead of the other removal options. Use a fine, metal cutting blade and take your time sawing, so as not to damage the toilet.
If removing stuck toilet bolts from the tank, drain the tank first by shutting off the water supply at the back of the toilet and holding the flush lever down until all the water drains out.