When there is a gap in the rock record (that nice series of layers deposited over time) there isn't an actual empty hole. We have to use clues in the rock to figure out that there is something missing. That gap is called an unconformity or disconformity.
Look in the picture to the right for the edge where a series of fine lines is cut off at an angle by a lighter layer of rock. The change of angle of the rock with one set of layers ending abruptly in a different type of rock is a big signal that something is missing between those two pieces of rock. Where the two types of rock meet is called a contact. There are several unconformities in this record, the others are harder to see - they are much more subtle!
The gap may represent a single event or a series of events. It might represent a loss of 100 years of information or it might represent a loss of millions of years of recorded time in that location. There is no way to tell what happened in the rock that is no longer present. This is one reason that ANDRILL and other drilling programs drill multiple cores, a section that might be missing in one core may not be missing in another core. If layers that are the same in both can be identified and matched up, then the missing pieces of time may be filled in between the two (or more) cores. See the diagram on the left for a simple illustration of this concept.
What might cause unconformities? Think about the types of things that might break down, move, or destroy rock.