The effect of lethal concentrations as 0.33 ppm, 0.26 ppm, 0.17 ppm and 0.09 ppm of tributyltin chloride on lipid content in ovary, hepatopancreas, gill and muscle of a freshwater prawn, Macrobrachium kistnensis for 24, 48, 72 and 96 hours respectively has been investigated. The result showed that TBTCl induces significant alteration in lipid metabolic profiles in ovary, hepatopancreas, gill and muscle after exposure to lethal concentration. The depletion in lipid content during exposure of different concentration of TBTCl might be due to its utilization in energy production by oxidation of lipids under the influence of lipase enzyme to derive fatty acids precursor for TCA cycle.