The analysis of derivatised iminosugars and other bioactive low molecular weight carbohydrates present at low concentrations in different vegetable extracts (hyacinth, mulberry and buckwheat) required the improvement of a previously developed gas chromatographic method. Among the different parameters optimized, the temperature of the injection port, evaluated for the first time, resulted to be the most important. Thus, 240 °C was chosen as a tradeoff to achieve the required volatility, to avoid degradation and to provide symmetric peaks for bioactive carbohydrates highly retained such as glycosyl inositols. GC-MS operating under selective ion monitoring (SIM) acquisition mode and GC-FID provided limits of detection and quantitation for the target compounds of 0.2 and 0.7 ng g(-1) and of 1 and 3 ng g(-1) on average, respectively. Therefore, both methodologies could be considered appropriate to extend the range of quantitation of these bioactives.