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Calculate runtime for a Java program

I want to calculate the runtime of my Java program. when i used the following method:

long startTime = System.currentTimeMillis();
           ...my program...
long endTime   = System.currentTimeMillis();
long totalTime = endTime - startTime;
System.out.println(totalTime);

the result is different from the time, so I'm going to get some (100 or some) samples and calculate the average value to make it more accurate:

long total = 0    
for (int i = 0; i < 100; i++) {
    Long s = System.currentTimeMillis();
    ...my program...
    Long e = System.currentTimeMillis();
    total += (e - s);
}

so I got the total runtime .. for the first method it is usually about 600 ms, and for the second method the result will be about 30,000 ms (so avg time: 30000/100 = 300 ms).

I think this may be due to the JVM, it takes some time to load a file or convert it to byte code. and the second method only load & convert once and just run the method 100 times?

I am not sure of my explanations, please correct me if I am wrong.

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