Biomarkers in exhaled breath condensate (EBC) and fractional exhaled nitric oxide (FeNO) have been widely evaluated in respiratory research as non-invasive methods of sampling the lungs. These methods are particularly attractive in lung transplantation (LTx) as they are simple, repeatable and sensitive. Chronic rejection, manifest by progressive airflow limitation and bronchiolitis obliterans syndrome (BOS), is currently the major limiting factor to long-term survival in LTx. Early detection of BOS and initiation of appropriate treatment could significantly improve survival. Exhaled breath biomarkers could allow early diagnosis of factors associated with chronic rejection. FeNO is elevated in LTx patients with infections and chronic rejection prior to clinical presentation, and several EBC biomarkers and volatile organic compound patterns also show promise in these areas. This review summarizes information on exhaled breath biomarkers in LTx and discusses their potential role in the management of LTx patients.