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Regression testing is an expensive part of the software maintenance process. Effective regression testing techniques select and order (or prioritize) test cases between successive releases of a program. However, selection and prioritization are dependent on the quality of the initial test suite. An effective and cost efficient test generation technique is combinatorial interaction testing, CIT, which systematically samples all t-way combinations of input parameters. Research on CIT, to date, has focused on single version software systems. There has been little work that empirically assesses the use of CIT test generation as the basis for selection or prioritization. In this paper we examine the effectiveness of CIT across multiple versions of two software subjects. Our results show that CIT performs well in finding seeded faults when compared with an exhaustive test set. We examine several CIT prioritization techniques and compare them with a re-generation/prioritization technique. We find that prioritized and re-generated/prioritized CIT test suites may find faults earlier than unordered CIT test suites, although the re-generated/prioritized test suites sometimes exhibit decreased fault detection.