For addressing the issue of adulteration and counterfeiting of the sources of origin for the edible bird’s nests (EBNs), a preliminary study of elemental characterization for their geochemical markers was performed. This study aims to characterize the elemental profiles as geochemical markers and evaluate the relationships between these markers which could be used for the verification of the geographical origin of EBN in Malaysia. EBN samples from house and cave nests that represent a range of geographical and environmental characteristics were analysed using Neutron Activation Analysis (NAA) technique. The method was validated by analysing the Standard Reference Material SRM-1515 (Apple Leaves) and SRM-1573a (Tomato Leaves) of NIST. A total of 18 elements were determined. The results showed a statistical analysis of one way ANOVA has proven that there have a significant different elemental profiles in both EBN, clearly V, As, Ba, Sc, Sm and Th were not detectable in the house EBNs. Therefore, initial finding could be concluded that those elements can be identified as the key elements for geochemical marker to differentiate the type of EBN. Furthermore the differnces probably due to natural presence of those elements as well as regional or location and seasonal variation factors affecting the dietry habits of the swiftlets.