How to measure time taken by Java code?

Say you have a particular method that you would like to put under the microscope. You can do that as follows:

long time1 = System.nanoTime();
thatMethod();
long time2 = System.nanoTime();
long timeTaken = time2 - time1;  
System.out.println("Time taken " + timeTaken + " ns");  

Computers are really fast so it may happen that time difference when using getTimeMillis() maybe zero. Hence, use nanoTime()

You can also use Caliper. They have a video to get started. Plus, thoroughly read the answer pointed to by creichen. It has a lot of great stuff in it.