Sesame was grown for two successive Khari-1 seasons (2008-2009 and 2009-2010) at the research field of Irrigation and Water Management Division, BARI, Gazipur. Two varieties namely BARI Til 2 and BARI Til 3 were used as test crop. The aim of the study was to assess the physiological reaction and yield reduction of the two varieties to water logging stress. A significant response of the crop in respect of water logging and its duration was observed for both the varieties. Seed yields were rapidly decreased as duration of logging increased. The trend of decrease in yield and deterioration of crop stand with water-logging was almost similar for both the varieties. Maximum yield decreases of 51.67% and 58.24% for a continuous 36 hours of water logging were observed for BARI Til 2 and BARI Til 3, respectively. Significant effect of duration of water logging on other agronomic parameters of the two varieties was also observed in the study. So farmers are suggested to remove the standing water from the field as early as possible to avoid drastic yield loss from water logging.