Use System.currentTimeMillis() or System.nanoTime() if you want even more precise reading. Usually, milliseconds is precise enough if you need to output the value to the user. Moreover, System.nanoTime() may return negative values, thus it may be possible that, if you're using that method, the return value is not correct.
A general and wide use would be to use milliseconds :
long start = System.currentTimeMillis();
...
long end = System.currentTimeMillis();
NumberFormat formatter = new DecimalFormat("#0.00000");
System.out.print("Execution time is " + formatter.format((end - start) / 1000d) + " seconds");
Note that nanoseconds are usually used to calculate very short and precise program executions, such as unit testing and benchmarking. Thus, for overall program execution, milliseconds are preferable.
