Background: Flow cytometry assay for PNH clone is a compulsory routine test for all aplastic anaemia patients. Objective: To estimate the frequency of PNH clone in aplastic anaemia. Method: Twenty-two known cases of aplastic anaemia patients were enrolled for the study. Flow cytometric quantitation of glycosyl phosphatidyl-inositol (GPI)-anchored proteins deficiency using markers CD14, CD24, CD45, CD59, Fluorescent Aerolysin (FLAER), CD235a (6 markers) were performed. Result: PNH clone was identified in 8 (36.4%) of the study population. Among PNH clone positive patients 7 (87.5%) were suffering from non-severe aplastic anaemia. Conclusion: PNH clone is significantly associated with aplastic anaemia and PNH clone assay should be regularly assayed in aplastic anaemia patients for specific management.