A siddha drug, linga chendhooram was prepared from cinnabar (lingam) and Citrullus colocynthis L. The transition of heavy metals concentration throughout theprocess were analysed to comprehend the significance ofdrug preparatory methods. In addition to that the main constituent cinnabar was purified from two different methods to comparatively analyse the significance of purification methods. Atomic absorption spectrometric studies were employed to obtain the concentration of class I heavy metals (lead, arsenic, cadmium and mercury) in all five samples- raw cinnabar (R), cinnabar purified (P1 and P2) from purification method 1 and 2, linga chendhooram (D1 and D2) prepared from P1 and P2. Based on the permissible limits given by The Ayurvedic Pharmacopoeia of India, except cadmium the concentrations of all other three heavy metals were found to be above the limit in P1, P2, D1 and D2. According to the oral Permitted Daily Exposure values for elemental impurities given in ICH Q3D(R1) Guidelines, D1 was within the permissible limits for both single and double oral doses whereas D2 showed a slight increase in the concentration of lead in a single oral dose itself. The drug preparatory method showed a reduction of the heavy metals concentration and comparative analysis of the purification methods revealed a substantial reduction of heavy metals concentration in the end drug D1 when compared with D2 showing that the methods of purification and drug preparation in siddha system plays a vital role in reducing the concentrations of heavy metals accordingly.