The increase in usage of heavy metals in different industrial activities causes their existence in effluents. Excessive concentrations of these heavy metals pollute soil and water. Heavy metals cause toxicities and other harmful effects not only in humans and animals but also in plants and soil microorganisms. Heavy metals disrupt many biochemical and physiological activities in bacteria, including growth, development, enzyme and hormone production. Indole acetic acid (IAA) is one of the most important hormones in plants, which is secreted by both bacteria and plants. The present study assessed the effects of Ni, Pb and Cu on the growth of Bradyrhizobium japonicum and IAA production.B. japonicum were grown in yeast mannitol broth in a rotary shaker at 100rpm for 18h for each variant. Ni, Pb and Cu with concentrations ranging from 2.5–40mg/L were added to B. japonicum cultures and turbidity was measured at 600nm. Effects of Ni, Pb and Cu on IAA production were determined by measuring the IAA content with Salkowski method. The metal uptake by B. japonicum was determined in the range of 5–50mg/L. A lettuce seedling assay was conducted to observe the effect of B. japonicum on plant growth under heavy metal stress. Lettuce seedlings inoculated with the bacterium were spiked with 5–500mg/L of Ni, Pb and Cu. Shoot and root length, and plant dry biomass were measured after 5days of germination.Bacterial growth was reduced with the increase of Ni and Cu concentrations. However, there was no significant growth effect with Pb in the considered range. The IAA production also followed the same pattern with Pb and Ni, but in the presence of Cu, IAA content was slightly increased and reached an equilibrium. The growth retardations observed in lettuce in the presence of Pb, Ni and Cu were in the decreasing order of Ni>Cu>Pb. Bacterial inoculation reduced the heavy metal stress and increased the shoot and root lengths of lettuce seedlings. FTIR spectrum of the bacterial biomass showed that amine and nitro groups are responsible in metal sorption process. The Pb-treated bacterial biomass showed a considerable difference in the FTIR spectrum compared to other treatments. According to our results, B. japonicum is sensitive to heavy metal stress with a retardation of growth and IAA production, though it is able to enhance the growth of lettuce seedlings under heavy metal stress.