Background: Gastrointestinal stromal tumors (GISTs) have malignant potential. Distinction of GISTs from leiomyoma is important to the decision of follow-up or treatment for upper gastrointestinal tract subepithelial lesions (SELs). There are few studies on the evaluation of gastrointestinal SELs with endoscopic ultrasound (EUS) elastography. Aims: To evaluate the efficiency of strain ratio (SR) measurement and Giovannini's classification (Gc) by EUS elastography in differentiating GISTs from leiomyomas. Materials and methods: Twenty-three lesions with histopathological diagnoses of 13 GISTs and 10 leiomyomas were evaluated. The lesions’ SR values were obtained from EUS reports retrospectively. Giovannini's classification was performed according to the elastography images recorded in the system. The effectiveness of SR and Gc in the distinction between GIST and leiomyomas was evaluated. Results: Twelve of the GISTs and 3 of the leiomyomas were with scores 4 and 5 according to Gc (p = 0.006). Gastrointestinal stromal tumors had a higher SR than leiomyomas (p = 0.001). For the diagnosis of GISTs, sensitivity/specificity/diagnostic accuracy were 92.3%/80%/87% for SR alone, 92.3%/70%/82.6% for Gc alone, and 84.6%/80%/82.6% for the use of both SR and Gc. Conclusions: This is the first study in which semi-quantitative (SR) and qualitative (Gc) methods were evaluated together for the distinction of GISTs and leiomyomas. The sensitivity of SR alone for diagnosing GIST is higher than that of Gc alone or the combination of both methods. Although SR alone does not diagnose GIST, it can be used as an auxiliary method in biopsy and follow-up decisions.