The collection and analysis of exhaled breath condensate (EBC) may be useful for the management of patients with chronic respiratory disease at all ages. It is a promising technique due to its apparent simplicity and non-invasiveness. EBC does not disturb an ongoing respiratory inflammation. However, the methodology remains controversial, as it is not yet standardized. The current diversity of the methods used to collect and preserve EBC, the analytical pitfalls and the high degree of within-subject variability are the main issues that hamper further development into a clinical useful technique. In order to facilitate the process of standardization, a simplified schematic approach is proposed. An update of available data identified open issues on EBC methodology. These issues were then classified into three separate conditions related to their influence before, during or after the condensation process: (1) pre-condenser conditions related to subject and/or environment; (2) condenser conditions related to condenser equipment; and (3) post-condenser conditions related to preservation and/or analysis. This simplified methodological approach highlights the potential influence of the many techniques used before, during and after condensation of exhaled breath. It may also serve as a methodological checklist for a more systematical approach of EBC research and development.