Neoadjuvant therapy is increasingly used in the treatment of gastrointestinal malignancies. New molecular target-specific agents also have a role in downstaging hepatic colorectal metastases and metastatic gastrointestinal stromal tumours. Pathologists need to be familiar with post-treatment changes and with tumour regression grading systems. Accurate assessment of specimens is crucial for prognostic purposes and to evaluate therapeutic response. A standardized pathological approach is recommended.