Carbon Nano Tubes could be either metallic or semi-conducting in nature, depending on their diameter. Its photocatalytic behavior has given an impetus to use it as an anti-microbial agent. More than 95% Escherichia coli and Staphylococcus aureus bacteria got killed when exposed to Carbon Nano Tubes for 30 minutes in presence of sunlight. Carbon Nano Tubes are supposed to have smooth surface on to which it accumulates positive charges when exposed to light. The surface that is non illuminated has negative charge. At the cellular level microorganisms produce negative charges on the cell membrane, Therefore damaging effect of multi walled carbon nano tubes (exposed to light) on the microorganisms is possible. In this paper, photo catalytic killing of microbes by multi walled carbon nano tubes is reported. Killing was due to damage in the cell membrane, as seen in SEM micrographs. Moreover biochemical analysis of membrane as well as total cellular proteins by SDS PAGE showed that there was denaturation of membrane proteins as well as total proteins of both the microbes studied. The killed microbes that showed a decrease in number of protein bands (i.e. due to breaking down of proteins) also showed an increase in level of free amino acids in microbes. This further confirmed that proteins got denatured or broken down into shorter units of amino acids. Increased level of free amino acids was recorded in both the microbes treated with multi walled carbon nano tubes and sunlight.