We determine the cost effectiveness of centre and home haemodialysis (HD), continuous ambulatory peritoneal dialysis (CAPD) and intermittent peritoneal dialysis (IPD) treatment in the Ministry of Health (MOH) programme. The viewpoint taken for this evaluation is that of MOH. Cost categories identified were capital cost, dialysis operational cost, medical cost and general hospital cost. Cost estimates were mostly based on actual resource utilisation. Life years saved were estimated based on Dialysis Registry data on 2480 HD and 732 CAPD patients. Overall, the cost-effectiveness ratio (CER) of centre HD was RM21620/life year saved. Those of home HD, CAPD and IPD were RM23375, RM30469 and RM36016 respectively. Sensitivity analyses did not change the ranking of the CER. We conclude the MOH dialysis programme was cost-effective, and among the various dialysis modalities centre HD was the most cost-effective.