The need for flexible and well understood knowledge representations which are capable of capturing clinical guidelines and protocols for decision support systems is widely recognised. PROforma is a method for specifying clinical guidelines and protocols in a form which can be executed by a computer to support the management of medical procedures and clinical decision making. The PROforma method comprises a graphical notation for designing protocols and a formal knowledge representation language to enable clinical concepts to be interpreted by a computer. This paper provides an overview of the motivation, structure and use of PROforma in developing computerised clinical guidelines.