This is a great question! Hand sanitizers are actually only effective at killing germs in certain situations. It is not effective if your hands are visibly dirty. In order for hand sanitizer to effectively kill germs, the sanitizer needs to contain above 60% of some kind of alcohol, and that the skin needs to be exposed for at least about 15 seconds to the alcohol in order for it to be effective. Typically, alcohols such as isopropanol, ethanol, or n-propanol are used as the active ingredients in hand sanitizers. Furthermore, it turns out that certain bacteria (the non-spore forming kind) are more susceptible to hand sanitizers than others.

So what is the mechanism that kills these bacteria? Alcohols kill germs by destroying the cell membranes and denaturing proteins of bacterial cells. Because of this, gram-negative bacteria (e.g. E. coli and salmonella) are more susceptible to sanitizers, since they have a thin peptidoglycan cell wall surrounded by an outer membrane, which can be dissolved by alcohols. Gram-positive bacteria (e.g. Staphylococcus) have a thicker peptidoglycan cell wall and are less vulnerable to alcohol-based sanitizers, but can still be killed by these sanitizers. There are some non-alcohol based sanitizers that are more effective against gram-positive bacteria, such as Benzalkonium chloride (BAC) based sanitizers.

But if you get a choice between washing your hands and using a hand sanitizer, you should probably opt for washing your hands with soap for at least 20-30 seconds. Why? The smaller the pathogen of interest (e.g. viruses are much, much smaller than bacteria), the easier it is for it to get trapped in the small crevices of your skin. Vigorous hand washing seems to be more effective at dislodging these germs, since in addition to the surfactants in the soap and the friction from rubbing your hands, there is the rinsing step, which does not occur when using hand sanitizer. Regular and frequent hand-washing is one of the most effective ways to reduce your chances of getting a cold or flu!