Grey scale median (GSM) measured on ultrasound images of carotid plaques has been used for several years now in research to find the vulnerable plaque. Centres have used different software and also different methods for GSM measurement. This has resulted in a wide range of GSM values and cut-off values for the detection of the vulnerable plaque. The aim of this study was to compare the values obtained with two different softwares, using different standardization methods, for the measurement of GSM on ultrasound images of carotid human plaques. GSM was measured with Adobe Photoshop(®) and with Artery Measurement System (AMS) on duplex ultrasound images of 100 consecutive medium- to large-sized carotid plaques of the Beta-blocker Cholesterol-lowering Asymptomatic Plaque Study (BCAPS). The mean values of GSM were 35·2 ± 19·3 and 55·8 ± 22·5 for Adobe Photoshop(®) and AMS, respectively. Mean difference was 20·45 (95% CI: 19·17-21·73). Although the absolute values of GSM differed, the agreement between the two measurements was good, correlation coefficient 0·95. A chi-square test revealed a kappa value of 0·68 when studying quartiles of GSM. The intra-observer variability was 1·9% for AMS and 2·5% for Adobe Photoshop. The difference between softwares and standardization methods must be taken into consideration when comparing studies. To avoid these problems, researcher should come to a consensus regarding software and standardization method for GSM measurement on ultrasound images of plaque in the arteries.