Primary graft dysfunction, a form of reperfusion pulmonary edema that occurs early after lung transplantation, shares key clinical and pathological features with acute lung injury and its more severe form, the acute respiratory distress syndrome. However, in contrast to acute lung injury/acute respiratory distress syndrome, in which biomarkers in plasma, urine and lung edema fluid have prognostic and pathogenetic value, the role of biomarkers in primary graft dysfunction has been less thoroughly explored. This review summarizes human and animal studies on biomarkers in primary graft dysfunction, including cytokines and markers of acute inflammation, VEGF, endothelial markers and adhesion molecules, markers of coagulation and fibrinolysis and markers of lung epithelial injury. Similarities to the literature in acute lung injury/acute respiratory distress syndrome are highlighted where appropriate, and future directions for research on the role of biomarkers in primary graft dysfunction are suggested.