The recent emergence of a highly lethal zoonotic virus, the Nipah virus, has raised concerns of a possible pandemic with high fatality ratios. While the similarities of the Malaysian and Bangladesh strains of the virus have been commented upon by various authors, the significant differences, if any, between the two strains that have led to starkly different fatality ratios of 40% and 75-100%, respectively, have not been satisfactorily addressed. In this report, we submit the results of our preliminary study of the strains as available from their complete genomes and show that the two strains are indeed different and should form part of a focused surveillance program.