If you set font-size:100% you are changing nothing because the font-size will be whatever the browser or user has set the font-size to. You can never know what that is.
The reason for using font-size:100% is usually to combat the scale bug in IE where text resizes at a strange rate unless the font-size is specified in percent for the root element.
Most browsers will probably default to 16px but there are just too many variables to be sure. In reality you shouldn't concern yourself with that anyway and you should make your layout work in whatever the user throws at it (easier said than done of course).
If you want a specific size (and ignoring accessibility issues) then you would need to set it in pixel measurements but even then the user may have set the browsers to ignore font sizes (colours and families) in their preferences or in their user stylesheets so you can never be certain.
As you don't really have any control then you should abandon control to the user and design accordingly