Transgenic tomato plants overexpressing LeFAD3 sense and antisense sequences were generated. Salt stress suppressed the growth of WT and antisense plants to a higher extent than that in sense plants. In this study, we investigated the role of the LeFAD3-encoding ER-type omega-3 fatty acid desaturase in salt tolerance in tomato plants. We created transgenic tomato plants by overexpressing its sense and antisense sequences under the control of the cauliflower mosaic virus 35S promoter. Based on the results of northern and western blotting as well as quantitative reverse transcription-polymerase chain reaction, sense plants expressed more desaturase than wild-type (WT) plants, whereas antisense plants expressed less desaturase than WT. Salt stress suppressed the growth of both WT and antisense plants to a higher extent than that in sense plants, which can be attributed to the fact that sense plants performed better in maintaining the integrity of the membrane system, as revealed by electron microscopy. The concomitant increase in superoxide dismutase (EC 1.15.1.1) and ascorbate peroxidase (EC 1.11.1.7) may have alleviated the photoinhibition caused by the increased level of ROS in sense plants. Our results suggest that LeFAD3 overexpression can enhance the tolerance of early seedlings to salinity stress.