An automated computer-based data integrity auditing system is provided for use in the healthcare industry, financial industry, academic and educational fields, or any other field in which a need exists for monitoring data integrity. Coded data received from a service organization are checked for proper coding and completeness. The coded data are stored in a computer database together with indicators specifying bad data found during the checking step. At least one data integrity test is applied to a portion of the data which does not have any bad data specified by an indicator. Any data validity problems located by the data integrity test(s) are identified. Reports may be generated to identify a score assigned to the tested portion of the data, the data validity problems, or suggestions for resolving the data validity problems.