This study investigates the partition of heavy metals in slag from the rotary kiln (SL), second combustion chamber ashes (SCCA), filter cake (FC) from a bag filter and flue gas (FG) emissions (both in particulate and gas phases) of the Istanbul medical waste incinerator (ISTAC). Eleven targeted heavy metals (As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, Sb and TO in four matrices were analysed for eight different date samples in 2008. The results obtained were evaluated according to the metal species, furnace temperatures and other factors that affect the formation and accumulation of the metals in the incineration cycle. According to the results, combustion temperatures, reactor configuration and waste contents are the dominant parameters determining the volatility and partitioning of metals in the combustion systems. The biggest waste portions were obtained for the SL and the dominant metal species for the SL and SCCA were Cu (505,9 +/- 99,3 and 697,4 +/- 577,7 mg per kg dry mass for SL and SCCA respectively) and Mn (238,0 +/- 154,6 and 199,9 +/- 180,4 mg per kg dry mass for SL and SCCA respectively). In the FC, the dominant species was Cu (166,8 +/- 128,1 mg per kg dry mass) and this was followed by Mn, Ni and Hg. It is thought that cement and activated lignite, which were added to the process as adsorbent materials, were affecting the contents of the FC. Metals were divided into particulate and gas phases and maximum concentrations were observed for Ni, Mn and Cr in a particulate phase of FG. Emission factors were considered and mass balance calculations for metals were also conducted in the study.