This study was subjected to analyse the technique for the determination of quercetin, a flavonoid in garlic (Allium sativum L.) from three different cultivars of bulb onion (G1, G2 and G3) which were extracted with petroleum ether, chloroform, methanol and water. Also this study was aimed to determine the antimicrobial activity of four solvent extracts of garlic cultivar against ten MTCC bacterial pathogens. Quercetin in garlic was determined by analytical technique, HPTLC and the antimicrobial activity was performed by well diffusion method. Quercetin was determined in all the three cultivars with Rf value 0.68. Quercetin was also extracted in all the four solvent extracts of garlic cultivars. Apart from quercetin, few more compounds also isolated. More compounds were isolated in G1. In the determination of antimicrobial activity of onion extracts against MTCC cultures revealed that onion cultivar was highly active against Staphylococcus aureus, it showed more than 25mm zone of inhibition. This study showed that onion has good broad spectrum bioactivity against microorganisms revealed that it contains phytochemicals which can be used as neutraceuticals.