Digestive system tumours are the most common malignancies worldwide, causing huge number of deaths each year. With the increases in morbidity and mortality, it is imperative to identify new therapeutic targets. Melanoma-associated antigen-A6 (MAGEA6) is a member of the cancer/testicular antigen (CTA) family. There are increasing amount of evidence supporting that MAGEA6 plays an important role in the development of solid tumours. However, there has been no comprehensive analysis of MAGEA6 in digestive system tumours. Therefore, our objective was to investigate the expression level, clinical significance and related biological functions of MAGEA6 in digestive system tumours. In this study, we integratively analysed the data from multiple databases of patients with digestive system tumours. Our results showed that MAGEA6 was highly expressed in most digestive system tumours as compared with normal tissues, whereas patients with higher expression of MAGEA6 had a worse prognosis. Based on co-expression analysis, there was a close interaction between MAGEA6 and MAGEA3. Furthermore, differential gene enrichment analysis indicated that MAGEA6 was mainly involved in the formation of extracellular structure, DNA replication, mitosis and the p53 signalling pathway. These results suggest that MAGEA6 is as a prognostic factor with functional importance in digestive system tumours.