Changes in microbiological and biochemical quality of clams (Ruditapes decussatus) subjected to low doses of gamma irradiation (0.5 and 1 kGy) were investigated during alive storage, at 5 °C. The mortality rate was significantly lower for irradiated clams compared with the control. In the same way, ammonia content was lower for irradiated clams (especially 1 kGy irradiated group). Considerable levels of total mesophiles, coliforms, staphylococcus, faecal streptococcus and Escherichia coli were detected in the control and irradiation had immediately reduced these charges; all bacteria studied experienced a 1- to 3-log reduction following 1 kGy irradiation. At the last day of storage, irradiated groups showed a noticeable reduction in the bacterial counts, whereas the mesophiles, staphylococcus and coliform germs were abundant in the control group (6.3, 2 and 1.7 log CFU g−1, respectively). Irradiation doses up to 1 kGy had not an immediate effect on fatty acids composition (P > 0.05) and lipid profile was better in irradiated samples, where polyunsaturated fatty acid fraction was maintained throughout storage using irradiation. Also, sodium dodecyl sulphate-polyacrylamide gel electrophoresis revealed minor changes in proteins bands between different samples. These results demonstrated that 1 kGy irradiation appeared to be the optimum dose for treating alive clams (R. decussatus), through improving the microbial quality and alleviating biochemical changes during refrigerated storage.