Edible bivalves such as cockles, clams, mussels and oysters are considered as an important protein sources among local population. However, allergy to these bivalves has also been increasingly recognized. Production of allergen extracts with high quality, efficacy and safety are very important, as this influences the outcome of the diagnostic tests of allergy. Thus, the aim of this study was to analyse the heavy metals and microcystin concentrations in local bivalves in order to produce bivalve allergen extracts with the lowest/acceptable toxic contaminants. Five species of local bivalves (Malaysian cockle, Asian green mussel, Asian clam, carpet clam and tropical oyster) from several locations in Kuala Lumpur and Selangor were selected in this study. Analysis of heavy metals in the bivalve samples was conducted by Induces Coupled Plasma-Mass Spectrometry (ICP-MS), followed by analysis of microcystin concentrations by qualitative and quantitative tests using the Abraxis Microcystin Test Strip and Abraxis-Microcystin ELISA kit, respectively. Concentrations of heavy metals and microcystin in these bivalve samples were then compared to the permissible limits recommended by Malaysia Food Regulation (1985). The concentrations of Pb, Sn, Hg, Cd and Sb from all bivalve samples were lower than the limits. However, high level of As was found in the tropical oyster and Asian green mussel collected from Wangsa Maju, Kuala Lumpur. Meanwhile, the qualitative test indicated all bivalves samples were negative for the presence of microcystin (0 ppb). In contrary, quantitative analysis of microcystin concentrations in all bivalve samples indicated either none or lower microcystin concentrations when compared to the WHO’s provisional tolerable daily intake (0.04 µg kg-1). Hence, as a conclusion, based on the results of heavy metal and microcystin concentrations analysis, Malaysian cockle, carpet clam and tropical oyster from Rawang, Asiatic hard clam from Wangsa Maju and Asian green mussel from Ampang were suitable to be selected as the allergen sources for production of allergen extracts in future studies. In addition, these results also indicated that all bivalve samples are safe for human consumption.