The duckweed bioassay was performed in small disposable pots to examine the allelopathic potential of aqueous extracts of Bt cotton and Non-Bt cotton in laboratory. Fifteen pots were set up with five replicates, each filled with different concn of leachate i.e. 1, 3 and 5% w/v. The experiment was run for 21 days. Both Bt and Non-Bt extracts were highly toxic to the growth of duckweed. Aqueous leachates of Bt were proved more toxic than non-Bt and reduced the growth of Spirodela polyrrhiza (L.) Schleid. The number of fronds of duckweed declined more than 95% in Bt and 86% in non Bt whereas dry weight up to 75% and 62% in Bt and Non-Bt cotton respectively after 21 days. This is the pioneer study on allelopathic potential of cotton.