Cyclosporine is one of the most vital agents in the process of successful allogeneic hematopoietic stem cell transplantation. Despite a long history and worldwide extent of cyclosporine use for prevention of graft versus host disease, currently there are lots of uncertainties about its optimal method of application to reach the best clinical outcome. A major portion of this problem stems from complicated cyclosporine pharmacokinetics. Study of cyclosporine pharmacokinetic behavior can significantly help recognition of its effectiveness and consequently, optimization of dosing, administration, monitoring and management of adverse effects. In this review, highly accredited but sparse scientific data are gathered in order to provide a better insight for preparation of practice guidelines and directing future studies for allogeneic hematopoietic cell recipients.