The use of computer simulations in education and training can have substantial advantages over other approaches. In comparison with alternatives such as textbooks, lectures, and tutorial courseware, a simulation-based approach offers the opportunity to learn in a relatively realistic problem-solving context, to practise task performance without stress, to systematically explore both realistic and hypothetical situations, to change the time-scale of events, and to interact with simplified versions of the process or system being simulated. However, learners are often unable to cope with the freedom offered by, and the complexity of, a simulation. As a result many of them resort to an unsystematic, unproductive mode of exploration. There is evidence that simulation-based learning can be improved if the learner is supported while working with the simulation. Constructing such an instructional environment around simulations seems to run counter to the freedom the learner is allowed to in ‘stand alone’ simulations. The present article explores instructional measures that allow for an optimal freedom for the learner. An extensive discussion of learning goals brings two main types of learning goals to the fore: conceptual knowledge and operational knowledge. A third type of learning goal refers to the knowledge acquisition (exploratory learning) process. Cognitive theory has implications for the design of instructional environments around simulations. Most of these implications are quite general, but they can also be related to the three types of learning goals. For conceptual knowledge the sequence and choice of models and problems is important, as is providing the learner with explanations and minimization of error. For operational knowledge cognitive theory recommends learning to take place in a problem solving context, the explicit tracing of the behaviour of the learner, providing immediate feedback and minimization of working memory load. For knowledge acquisition goals, it is recommended that the tutor takes the role of a model and coach, and that learning takes place together with a companion. A second source of inspiration for designing instructional environments can be found in Instructional Design Theories. Reviewing these shows that interacting with a simulation can be a part of a more comprehensive instructional strategy, in which for example also prerequisite knowledge is taught. Moreover, information present in a simulation can also be represented in a more structural or static way and these two forms of presentation provoked to perform specific learning processes and learner activities by tutor controlled variations in the simulation, and by tutor initiated prodding techniques. And finally, instructional design theories showed that complex models and procedures can be taught by starting with central and simple elements of these models and procedures and subsequently presenting more complex models and procedures. Most of the recent simulation-based intelligent tutoring systems involve troubleshooting of complex technical systems. Learners are supposed to acquire knowledge of particular system principles, of troubleshooting procedures, or of both. Commonly encountered instructional features include (a) the sequencing of increasingly complex problems to be solved, (b) the availability of a range of help information on request, (c) the presence of an expert troubleshooting module which can step in to provide criticism on learner performance, hints on the problem nature, or suggestions on how to proceed, (d) the option of having the expert module demonstrate optimal performance afterwards, and (e) the use of different ways of depicting the simulated system. A selection of findings is summarized by placing them under the four themes we think to be characteristic of learning with computer simulations (see de Jong, this volume).