Small submucosal tumors (SMT) without symptoms are frequently found by endoscopic and radiological examinations. To find proper diagnostic measures and therapeutic indications for histologically undiagnosed SMT, we reviewed published articles in PubMed between 1990 and March 2013 using the key words ‘submucosal tumor’ and the name of a specific disease. SMT is observed in a wide range of gastrointestinal (GI) diseases and conditions, including compression by extra-GI organs and lesions, congenital tumors, inflammation, and benign as well as malignant neoplastic lesions. In the diagnosis of diseases and decision-making for therapy, endoscopic ultrasonography (EUS) and endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) may play a key role. Symptomatic SMT and SMT histologically diagnosed as malignant or potentially malignant tumors such as gastrointestinal stromal tumor (GIST) should be treated by surgery. SMT >5 cm, SMT increasing in size and those with‘high-risk features’ including irregular border, heterogeneous internal echo such as anechoic area, and heterogeneous enhancement by contrast media may also be removed by surgery. Laparoscopic approach is feasible for gastric GIST <5 cm and this is considered less invasive than the open approach. Emerging techniques using flexible endoscopes appear less invasive, but require further evidence and are still under clinical study. Correct diagnosis of SMT is challenging; however, EUS and EUS-FNA are useful in the histological diagnosis and clinical decision-making. In the future, minimally invasive approaches may be a mainstream of surgical treatment for small SMT.