Common and distinct genetic alterations are involved in the multistep mechanism of gastrointestinal carcinogenesis. Inactivation of the p53 and APC genes, activation of teleomerase and anomalous CD44 expression are common events that serve as a genetic marker for differential diagnosis of cancer. Amplification of cyclin D1 gene is preferentially found in esophageal cancer, whereas cyclin E gene amplification is frequently associated with both gastric and colorectal cancers. Multiple genetic alterations differ depending on the two histological types of gastric cancer. These genetic alterations can be applied in the multistep mechanism of the development and progression of gastrointestinal cancers. By application of these observations in clinical practice, we can facilitate and improve the differential diagnosis on cancer, obtain information on the grade of malignancy, determine patient prognosis, and identify patients at high risk for developing multiple cancers.