|MadSci Network: Chemistry|
Some molecules such as DNA are so big that one can see them under an electron microscope. Others are not quite as big, but if you attach a metal tag to them you can see them under an electron microscope. Still other molecules are even smaller and the only way one can see them is to shoot X-rays at them and observe how molecules of different shapes deflect the X-rays in different manners (similar to how healthy teeth and teeth with cavities will deflect X-rays in different ways). Finally, some molecules are very small and scientists know they exist by "inference." In other words, they know that these molecules exist because they can take a piece of a compound big enough to hold in your hand and do various experiments on it, and the best way to explain the results of those experiments is to postulate that the compound is made up of many tiny structures called molecules which are all the same and add up to give the properties that you observe for the substance as a whole.
Try the links in the MadSci Library for more information on Chemistry.