Warren Weaver, writing about the function that science should have in mankind’s developing future, ideas and ideals, proposed to classify scientific problems into ‘problems of simplicity’, ‘problems of disorganised complexity’, and ‘problems of organised complexity’ — the huge complementary class to which all biological, human, and social problems belong. Problems of simplicity have few components and variables and have been extensively addressed in the last 400 years. Problems of disorganised complexity have a huge number of individually erratic components and variables, but possess collective regularities that can be analysed by resourcing to stochastic methods. Yet, problems of organised complexity do not yield easily to classical or statistical treatment since interrelations among phenomenon elements change during its evolution alongside commonly used state variables, affecting behaviour and outcome. Moreover, organisation, the focal point in this complementary class, is still an elusive concept despite the gigantic efforts undertaken since a century ago to tame it. This paper addresses the description, representation and study of phenomena in the ‘problems of organised complexity’ class. Grounded on relational mathematical constructs, a theoretical framework providing operational definitions and schemes for formally modelling organisations and interaction of organisations is introduced. This framework extends the general systems’ concept and provides a novel perspective for addressing organised complexity phenomena as a collection of interacting organisations.