Proteinase inhibitor II (T-pinII) has been employed as terminator sequence in 25% of globally approved genetically modified (GM) crops (maize, potato, tobacco). Loop-mediated isothermal amplification (LAMP) is a rapid method for detection of genetically modified organisms (GMOs) that amplifies the targeted region with high specificity and sensitivity under isothermal conditions. Visual and real-time LAMP assays targeting T-pinII terminator sequence were developed for screening of GM crops/events. Specificity and sensitivity of these assays were confirmed using a set of 17 samples including GM events of three GM crops, namely, maize, soybean and cotton along with the non-GM counterpart as respective targets and non-targets. Limit of detection of visual LAMP was established up to 0.01% equivalent to 7 target copies. LAMP assay on the isothermal real-time system was found sensitive enough to detect as low as 7 target copies within 40 min. Stability of visual LAMP was also assessed in terms of shelf life of reagents by storing them for a period from 1 to 15 days at different temperatures. No significant difference was found in the performance of LAMP among the reagents stored at − 20 °C (recommended storage temperature), 4 °C, 25 °C, 30 °C, 37 °C, whereas at 42 °C, the stability was reduced detecting only 1.0% of target up to 4 days only. The LAMP assays herein presented can be effectively utilized for rapid and cost-effective screening for the GM status of a sample for respective GM events, as well as for on-site application.