This report contains complete documentation for the 15 programs and 11 data files of the EPA Atomic Absorption Instrument Automation System. The system incorporates the following major features: (1) multipoint calibration using first, second, or third degree regression or linear interpolation, (2) timely quality control assessments for spiked samples, duplicates, laboratory control standards, reagent blanks, and instrument check standards, (3) reagent blank subtraction, and (4) plotting of calibration curves and raw data peaks. The programs of this system are written in Data General Extended BASIC, Revision 4.3, as enhanced for multi-user, real-time data acquisition. They run in a Data General Nova 840 minicomputer under the operating system RDOS, Revision 6.2. In this document there is a functional description, a symbol definitions table, a functional flowchart, a program listing, and a symbol cross reference table for each program. The structure of every data file is also detailed. Two related publications are 'The Standard Calibration Instrument Automation System for the Atomic Absorption Spectrophotometer Part I - Functional Specifications' and 'The Standard Calibration Instrument Automation System for the Atomic Absorption Spectrophotometer Part II - User's Guide.'