Tefillin should be checked every 3.5 years to ensure that they are Kosher. Many Rabbis have reccomended that they be checked every year. There are many things that the Sofer(scribe) will look for when he checks your Tefillin. The two basic categories are: Damage that may have occurred do to water, heat etc. and problems in the way the Tefillin was written such as spelling mistakes, touching letters, improper spacing etc.
If a problem is found, the Sofer has to determine if it can be corrected or not.
Checking Tefillin requires the Sofer to check the Batim and Retzuos, to insure that they are Kosher. Unfortunately, many sofrim only check the scrolls but not the other parts of the Tefillin.
Tefillin checking tends to be much more expensive than Mezuzah checking because the Sofer has to re-assemble and sew shut the Tefillin. This is a time consuming process.