Paroxysmal nocturnal haemoglobinuria is a clonal, acquired disease affecting the membrane of the blood cells, arising from a somatic mutation at the haematopoietic stem cell level. It results in clones of blood cells deficient in membrane bound proteins, such as the complement regulating molecules Decay Accelerating Factor (DAF = CD55) and Membrane Inhibitor of Reactive Lysis (MIRL = CD59). For many years, Ham's test has been essential for diagnostic testing of erythrocytes for paroxysmal nocturnal haemoglobinuria. We present a 3-colour flowcytometry method used for quantification of CD59-negative erythrocytes and CD55/CD59-negative leukocytes. The results from analysis of blood samples from six patients suffering from paroxysmal nocturnal haemoglobinuria and six healthy blood donors, using the flowcytometry method, Ham's test and a microtyping gelcard method are compared. Our flow cytometric method, using directly conjugated monoclonal antibodies to test both erythrocytes and leukocytes, is the most sensitive method. It is specific and delivers fast results. The method involves a minimum of manipulation of the fragile cells and can be recommended as an alternative to Ham's test and the gelcard test.