Is the 'check engine' light on? If it's not a mechanical issue like valve adjustment or a rod/bearing knock, as the other response addresses , it may be normal 'piston slap' which would get quieter as it warms up. That motor does not have a distributor , so if it is actually pre-ignition or 'spark knock' you may have a faulty knock sensor or a vacuum leak somewhere , causing a 'lean' condition. Need to know more specifics on conditions to properly answer. May be best to have a shop scan 'live data' and check fuel trim for starters. Also TPS for proper values.
is it more of a thud, or a double click and how long has been since u changed you oil, check the oil level. does it get louder with rpms, and is louder when its cold and then gets some what quiter when the engine gets warm