An Integrated Learning System (ILS) is an advanced computer-based instructional system, generally consisting of a set of computerized courseware covering several grade levels and content areas, and complex classroom management and reporting features. Although ILSs have become increasingly popular in schools over the past five to ten years, they introduce several potential factors that could have negative effects on students' academic and social growth. These factors include: (a) de-emphasis of affective outcomes and increased student isolation, (b) lack of teacher involvement in curriculum planning and delivery, and (c) disparate effects on student achievement based on students' academic level. One possible strategy for addressing these concerns is integrating cooperative learning with ILS instruction. This paper will examine the research dealing with integrating cooperative learning strategies and computer-based instruction and provide guidelines and strategies for designing ILS instruction that enhances opportunities for cooperative learning.