Business to Business (B2B) relationships in E-commerce are becoming increasingly important. However, there is little guidance available for managers about how relationships should be formulated or managed. Further, requirements analysis for information technology support of B2B inter-organisational relationships (IORs) depends on the business model of the relationship, and needs a predictive basis. This paper describes a method for planning and managing IORs based on Williamson's transaction cost theory, to guide managers when negotiating B2B alliances, and procurement of IT support for them. This method covers market analysis, relationship planning, transaction cost estimation and IT requirements analysis. Lessons learned in presenting the method to managers and using it in case studies are reviewed.