When you remove a toilet, you expose the flange and open drain. A viable concern is the entrance of fumes into the room before the replacement toilet is installed.
The colorless, but definitely foul, fumes that arise when the toilet is removed are sewer gases. These strong gases are not simply an annoyance that comes with the territory when replacing a toilet. Hydrogen sulfide and often methane, along with other chemicals and biological agents in varying degrees, compose sewer gas. The fumes of this gas pose definite health risks, especially if inhaled for an extended period of time.
Not only is methane explosive, it displaces oxygen. Reduced oxygen levels can lead to lethargy. Also, hydrogen sulfide, which is the result of decomposing organic matter, is fatal to humans and animals within seconds or minutes if large concentrations of it is inhaled, according to the U.S. Environmental Protection Agency.
Prevent sewer gases and the overpowering fumes from creeping up through the drain pipe by stuffing a rag into the drain opening. Remember to remove the rag before installing the new toilet. Also, be sure to properly install a wax ring on the toilet horn before installation. This wax seal protects against sewer gases and water leaks from entering from beneath the toilet after it is installed.