Currently, therapeutic management of gastric cancer is mainly based on clinical data and histological features. Although several new treatment options have recently been introduced, inter-individual variability of response and drug resistance are still a challenge. Many promising markers have been identified to predict prognosis and likelihood of response to therapy, in order to tailor treatment regimens on the basis of patients' individual features. However, despite recent developments in gene sequencing and molecular diagnostics, many biomarkers still have a controversial role. Published data are often contradictory and at the moment, no molecular marker, other than Human epidermal growth factor receptor-2 (HER2) status for trastuzumab-based treatment, has entered the mainstream of clinical practice. The primary obstacle to the identification of reliable markers lies in technical difficulties in quantitatively assessing molecular alterations; genome-wide analyses are also often misleading due to the complexity of biological processes. Nevertheless, many biomarkers are being evaluated in clinical trials in order to identify criteria for stratifying patients and establish customized therapeutic approaches. In this review, we provide an update on promising biological prognostic and predictive markers, with a focus on growth factor signalling molecules, DNA repair systems, fluoropyrimidine metabolism and apoptotic pathways.