Venous thromboembolism (VTE), which mostly includes deep vein thrombosis (DVT) and pulmonary embolism (PE), is associated with considerable morbidity and mortality in patients with cancer. As little is known about VTE associated with gastrointestinal cancers among the populations in the Middle East. This study aimed to determine the relative frequency of symptomatic VTE in patients with gastrointestinal malignancies in Iran. The charts of patients with gastrointestinal cancers in our institute from April 2010 to March 2015 were investigated for symptomatic VTE in a retrospective study. In this study, all of the patients received chemotherapy. The data included the site of cancer, time of therapies initiation, patient's characteristics, type of VTE, the time of developing symptomatic VTE of patients with gastrointestinal cancer and the stage which VTE occurred. All of DVTs and pulmonary embolism were confirmed by Doppler ultrasonography and computed tomography angiography. A total of 614 consecutive patients with gastrointestinal cancer were included in study. In total, 22 patients (3.6%) were found to have experienced symptomatic VTE (confidence interval 95%: 2.1–5.1%) which included: 19 patients who suffered from DVT and three of them detected pulmonary embolism, and other types of VTE were not reported. Out of 22 patients with VTE, 17 of them have been occurred after chemotherapy (77%) within 6.17 ± 5.17 (range, 1–19) month after starting chemotherapy. The distribution of frequency of stage in which the VTE occurred, was more in stage III and IV. The rate of symptomatic VTE in patients with gastrointestinal cancer in Iran is relatively lower than other studies done in the west. Therefore, it seems the rate of VTE differs in different ethnic groups.