Do you mean for synching between two folders? Use Tools -> Synchronize Panel for that.
If you mean you want to compare two arbitrary files, which could be two files in the same directory, to see if they're the same, Opus doesn't have a built-in tool for that. There are a bunch you can integrate into Opus, though.
The most simple (and ugly 
) way to get that is to use the "fc" (file compare) command built into windows. It's ugly because the result is shown in a command prompt window. My Diff/Merge Toolbar includes a button which runs fc. (It's the "Bin F" button on the toolbar.)
A better way is to use something like Beyond Compare, which works great with Opus. BC is usually used for diffing text files but it can compare binary files as well. It'll also show you what the differences are (as a hex view), not just whether or not the files are the same.
There are other diffing tools as well but I'm not sure which of them are good for binary files.