Iodine Deficiency Disorders (IDD) are a common health problem prevalent in the wet zone of Sri Lanka with a prevalence of >25% of the population. In comparison, in the dry zone of Sri Lanka IDD occurs in <10% of the population. Seventy soil samples from 14 villages selected on the basis of the incidence of goitre, were collected and analysed for 13 trace elements using ICP-MS. In order to identify any prevailing differences in antecedent chemical environments, soil samples from each pre-selected village were classified into three groups in terms of their geographical location. Among the elements investigated, the total soil concentrations of Rb, Sr, Ba, Mn and Co are lower in the wet zone of Kalutara. In contrast, total soil Rb, Sr, Ba and Mn contents are higher in the dry zone of Anuradhapura. Further soil total Mo and Nb levels are relatively similar in all pre-selected study locations. The high endemic goitre regions (IDD >25% of the population) show low levels of Rb, Sr, Ba, and Mn and higher levels of V, Cr, Co, Ni, Cu, Zn and Pb as compared with moderate and non-goitre areas. Factor analysis was used to exploit the correlation structure present in data and yielded three groups in all cases. This indicated that most transition group elements and iodine are associated with the Mn phase in the low IDD areas whereas iodine shows a high affinity for the organic phase in high IDD regions. The variable distribution of trace elements, therefore, must be due to differences in mobility and capacity for incorporation into the structure of secondary minerals or organic phases.