In recent years, several studies have focused on antioxidant, anti-inflammatory, and anti-cancer activities of quercetin (3,3′,4′,5, -pentahydroxyflavone). The nanotization of quercetin was shown to enhance its therapeutic efficacy due to smaller particle size. In the present study, an additional step was added to simple extraction cum RP-HPLC method for the quantification of nanotized quercetin (nQ) in biological samples to understand the pharmacokinetics and biodistribution of nQ following intravenous administration. The proposed method involves extraction of nQ from blood serum and tissues of mice with 2N HCl in comparison to well-known DMSO:MeOH mix method. The HCl extraction was found to be 2 – 3 times more efficient than DMSO:MeOH mix method. Results showed that the amount of nQ at various time intervals in the serum and tissues was 2 – 3 fold greater for HCl extraction than for DMSO:MeOH mix method, suggesting that HCl extraction must take into account nQ bound with protein. The reversed-phase HPLC was used for nQ detection, which showed the nQ retention time of 3.2 min. The limit of detection of nQ in blood serum was found to be 0.1 μg/mL. The proposed method was also validated in terms of linearity, precision, and accuracy.