Due to large quantities of bacteria and viruses in toilets after use, it's polite to close the toilet lid while flushing. Since these microbes are especially threatening to the health and comfort of your family and guests, it's also important to place soap in the bathroom for your guests' immediate use after handling the toilet seat, lid and handle.
Leaving the toilet seat lid up is generally regarded as poor etiquette regardless of the type of business you've just done. This is because the aerosol effect created when you flush with an open lid can spread both viruses and bacteria throughout a bathroom for hours after the flush. These microbes can make you sick, especially if they land on your toothbrush.
While the toilet seat lid does prevent microbes from circulating around the bathroom, some consider it polite to leave the toilet lid up and the toilet seat down when expecting guests. This is to prevent the guest from having to lift the toilet seat lid prior to use. The guest should place the lid in the down position after use.
If you have recently cleaned the toilet bowl thoroughly, it is acceptable to leave the lid in the up position to make toilet use more convenient for the next person to use it. The germs in the toilet have presumably been killed by the chemicals in cleaning. When cleaning, always include each side of the toilet lid in addition to the toilet bowl to prevent the spread of germs.
Parents should teach proper toilet etiquette to children by purchasing a training toilet with a lid. Parents can instruct children to close the lid after finishing with the toilet.
Cleaning before guests arrive is most polite. Those especially concerned with the health and safety of family and guests may purchase an antibacterial toilet seat and lid. Best etiquette also dictates leaving antibacterial soap and antibacterial lotion in the bathroom.