Basmati rice is a very special type of aromatic rice known world-wide for its extra long grains and pleasant and distinct aroma. Traditional Basmati rice cultivars, confined to Indo-Gangetic regions of the Indian subcontinent, are often reported to be adulterated with crossbred Basmati varieties and long-grain non-Basmati varieties in the export market. At present, there is no commercial scale technology to reliably detect adulteration. We report here a CE-based multiplex microsatellite marker assay for detection as well as quantification of adulteration in Basmati rice samples. The single-tube assay multiplexes eight microsatellite loci to generate variety-specific allele profiles that can detect adulteration from 1% upwards. The protocol also incorporates a quantitative-competitive PCR-based analysis for quantification of adulteration. Accuracy of quantification has been shown to be ±1.5%. The experiments used to develop and validate the methodology are described.