There are two standards that you should already be familiar with.
Sterilization is the killing of ALL pathogens, and takes place at temperatures above boiling water for a number of minutes (why you can't do home bottling or canning without a pressure cooker).
Pastuerization kills MOST of the pathogens by heating at or above 161F for a few seconds.
At boiling water temperatures, you can't kill everything. But the idea is that you kill almost everything and what's left is in small enough quantities that your body's immune system will handle it without symptoms appearing. Assuming that we are dealing with relatively pure water (you didn't get it from a cesspool), a trip to the boiling point should be sufficient. Actually, just taking it above 161F is sufficient to kill the majority of bugs, but seeing the water boil ensures it's above 161F without carrying around a thermometer.
(Added info) Here's an
REI article that says:
"Most medical experts we interviewed, however, argue that simply bringing water to a boil is sufficient. Boiling water for several minutes is considered excessive. For details, see the "Boiling" section of our Water Treatment for International Travel article."
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