System.currentTimeMillis vs System.nanoTime

If you're just looking for extremely precise measurements of elapsed time, use System.nanoTime(). System.currentTimeMillis() will give you the most accurate possible elapsed time in milliseconds since the epoch, but System.nanoTime() gives you a nanosecond-precise time, relative to some arbitrary point.

From the Java Documentation:

public static long nanoTime()

Returns the current value of the most precise available system timer, in nanoseconds.

This method can only be used to measure elapsed time and is not related to any other notion of system or wall-clock time. The value returned represents nanoseconds since some fixed but arbitrary origin time (perhaps in the future, so values may be negative). This method provides nanosecond precision, but not necessarily nanosecond accuracy. No guarantees are made about how frequently values change. Differences in successive calls that span greater than approximately 292 years (2⁶³ nanoseconds) will not accurately compute elapsed time due to numerical overflow.

For example, to measure how long some code takes to execute:

long startTime = System.nanoTime();    
// ... the code being measured ...    
long estimatedTime = System.nanoTime() - startTime;

See also: JavaDoc System.nanoTime() and JavaDoc System.currentTimeMillis() for more info.

Update by Arkadiy: I've observed more correct behavior of System.currentTimeMillis() on Windows 7 in Oracle Java 8. The time was returned with 1 millisecond precision. The source code in OpenJDK has not changed, so I do not know what causes the better behavior.

David Holmes of Sun posted a blog article a couple years ago that has a very detailed look at the Java timing APIs (in particular System.currentTimeMillis() and System.nanoTime()), when you would want to use which, and how they work internally.

Inside the Hotspot VM: Clocks, Timers and Scheduling Events - Part I - Windows

One very interesting aspect of the timer used by Java on Windows for APIs that have a timed wait parameter is that the resolution of the timer can change depending on what other API calls may have been made - system wide (not just in the particular process). He shows an example where using Thread.sleep() will cause this resolution change.

System.nanoTime() isn't supported in older JVMs. If that is a concern, stick with currentTimeMillis

Regarding accuracy, you are almost correct. On SOME Windows machines, currentTimeMillis() has a resolution of about 10ms (not 50ms). I'm not sure why, but some Windows machines are just as accurate as Linux machines.

I have used GAGETimer in the past with moderate success.

Yes, if such precision is required use System.nanoTime(), but be aware that you are then requiring a Java 5+ JVM.

On my XP systems, I see system time reported to at least 100 microseconds 278 nanoseconds using the following code:

private void test() {
    System.out.println("currentTimeMillis: "+System.currentTimeMillis());
    System.out.println("nanoTime         : "+System.nanoTime());
    System.out.println();

    testNano(false);                                                            // to sync with currentTimeMillis() timer tick
    for(int xa=0; xa<10; xa++) {
        testNano(true);
        }
    }

private void testNano(boolean shw) {
    long strMS=System.currentTimeMillis();
    long strNS=System.nanoTime();
    long curMS;
    while((curMS=System.currentTimeMillis()) == strMS) {
        if(shw) { System.out.println("Nano: "+(System.nanoTime()-strNS)); }
        }
    if(shw) { System.out.println("Nano: "+(System.nanoTime()-strNS)+", Milli: "+(curMS-strMS)); }
    }