Background Guggulu is an oleo gum resin obtained from the plant Commiphora wightii (Arn.) Bhand., used in Ayurved ic medicines for various ailments like anti-inflammatory conditions, hyperlipidemia, thyroid disorders etc. Guggulsterones E & Z are responsible for these broad ranges of pharmacological actions. It is recommended to do Shodhana (purification) before incorporating it into medicinal formulations. Sahasrayoga, an Ayurvedic text, emphasizes the purification of Guggulu in a particular media, which is a long run practice in Kerala. Objectives To compare the physicochemical and phytochemical parameters, quantitative estimation of Guggulsterone E & Z using high performance thin layer chromatography (HPTLC) and qualitative gas chromatography-mass spectrometry (GC-MS) analysis of Guggulu before and after purification. Methods Shodhana of Guggulu was performed in Water boiled with crushed fresh leaves of Neem (Azadirachta indica) and fresh rhizome of turmeric (Curcuma longa) using a special equipment (Dolayantra). Preliminary physicochemical and phytochemical evaluation, quantification of Guggulsterones E & Z using HPTLC and GC-MS analysis of raw and purified Guggulu were performed. Results Phytochemical evaluation of metabolites revealed marked variations. The mean concentrations of Guggulsterone E & Z showed significant differences before and after purification (p<0.01). On GC-MS analysis, it was found that few new compounds were added in the purified Guggulu. Conclusions Therapeutic efficacy of Guggulu might have enhanced after traditional purification.