Oesophageal and oesophagogastric junction cancers represent a significant burden to public health. Clinical practice guidelines recommend treatment based on cellular and molecular targets from tissue obtained before initiating therapy, including human epidermal growth factor receptor, microsatellite instability, mismatch repair, programmed death-ligand 1 and neurotrophic receptor tyrosine kinase gene fusions. The expression of these markers and the detection of circulating tumour cells and DNA in oesophageal and oesophagogastric junction cancers are temporally variable following treatment. Together, these findings may help individualize treatment and stratify patients at high risk of disease progression and recurrence.