A polar molecule is any molecule that has points where there is an overall difference of electronegativity that set up slightly positive and slightly negative areas. These slightly positive or slightly negative areas act almost like regular charges. For example, a slightly negative area is not inclined to interact with another slightly negative area, but it is likely to interact with a slightly positive area.
The most important representative polar molecule is water. Water has a significant difference in electronegativity between the oxygen and hydrogen atoms, making it very polar. In fact, because water is so plentiful in our body and because water is so polar, it sets up the important aspects of every other polar and nonpolar molecule.
The other polar molecules in the body would rather interact with other polar molecules than with nonpolar molecules. So, if you have a molecule of sugar that has polar parts, those polar parts tend to interact with water. In this case, the partial negatives on the sugar interact with the partial positive hydrogens in the water, and vice versa.
Nonpolar molecules in the body, such as lipids, tend to minimize the surface area available to polar molecules, like water. This effect maximizes entropy in the system and helps the body create important structures, like cell membranes.
The best, easiest way to to remember why this is important is to remember that water is the most abundant molecule in the body. It acts as the solvent for almost every other molecule in it. Polar molecules like to be near it, and nonpolar molecules tend to stay away from it in a shell.