You should not ignore bubbles coming up from a toilet's drain opening since the presence of air bubbles in a toilet's drain indicates at least a minor problem. Clogs in the toilet's drain line, or the vent pipe for the entire bathroom, will cause the bubbles to come up through the toilet's drain opening.
Toilets develop clogs when waste material or toilet paper crowd the drainpipe, sticking in place so water does not flow down the drainpipe as it normally would. Foreign objects flushed down the drain will also lead to clogs in the toilet's drainpipe. A partial clog, or one that still allows some water to flow down the drainpipe, will sometimes trap air behind it, leading to bubbles coming out of the toilet's drain opening.
Every plumbing fixture in your house should connect to a vent pipe; otherwise the fixture will not have a balanced exchange of air. Air flows down the drainpipe each time you flush the toilet, but the vent pipe connected to the toilet's drainpipe pulls air from outside the house to replace the lost air. As long as the vent pipe does not have a clog or damage that keeps it from functioning properly, you will not see problems with bubbles or other air coming up the toilet's drain.
Fixing the Problem
As long as the toilet's vent pipe does not have a major clog, clearing an obstruction from the pipe lies within the ability of an average homeowner. You must use a ladder to climb onto the house's roof since that is where the vent pipe openings are. The clog may consist of a tennis ball, sticks or leafs that have fallen down the vent pipe and accumulated. Pull out any obstructions you can reach using a long screwdriver or other tools. For clogs you cannot reach to pull out, dislodge the clog material by shooting water down the vent pipe using your garden hose. If you have a drain snake, feed the snake down the vent pipe, which will also push the clog free.
Calling in Help
When you have tried everything in your power to clear clogs from the toilet's drain and vent pipe, and yet the bubbles continue to come up from the toilet's drain, you need to turn to a professional plumber for help. Paying for a plumber's services will help you avoid more serious problems with your house's plumbing in the near future, since the bubbles likely are coming from a large clog in the house's plumbing. A plumber has special devices to help him locate the clog and eliminate it without damaging your house's plumbing.