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Both real-time PCR and digital PCR are being used for quantitative analysis of genetically engineered (GE) traits. The quality and quantity of DNA varies according to the method used for DNA extraction. There is no information on the impact of different DNA extraction methods on digital PCR for absolute quantification of GE traits. Fast DNA extraction methods are preferred in terms of saving time and resources. Seven Commercially available and relatively fast DNA extraction kits were evaluated for their suitability to quantify GE traits using digital and real-time PCR. Ground seed samples spiked at 0.1% level were used for analysis of three GE events in canola, flax and soybean. RainDropTM Digital PCR system and ABI 7500 were used for digital and real-time PCR, respectively. Sufficient amount of DNA was obtained for digital and real-time PCR use for most of the kits. One of the kits was not suitable for extraction of DNA from ground samples for all three crops. All DNA extracted using the commercial kits had low Abs260/230 ratios; while some of the DNA had acceptable Abs260/280 ratios. Canola and soybean DNA extracted with many of the kits was suitable for both digital and real-time PCR and the expected 0.1% percentage values were obtained. Flax DNA extracted with many of the kits was viscous and few and erratic target droplets were generated for digital PCR. The information is useful for laboratories involved in analysis of GE traits using digital and real-time PCR.