Most of it is written in a custom language called HAL/S (High Level Assembly Language / Shuttle). Some of the nitty gritty is written in assembly.

HAL/S looks a little bit like basic or FORTRAN. It was designed to be very readable and uses some interesting formatting. When you print out a module (lets say GG1ASC), it uses three lines for each line of code so that the superscripts and subscripts are above and below like they should be.

I have heard that Ada is popular in systems such as this, although I'm not sure if its actually used in here.