Chronic obstructive pulmonary disease (COPD) is a common, complex and heterogeneous condition which is responsible for considerable and growing morbidity, mortality and healthcare expense worldwide. In order to decipher the complexity of COPD, it is imperative that we identify groups of patients with similar clinical characteristics, prognosis and/or therapeutic needs, so called clinical phenotypes. This strategy is logical for research but it may be of limited clinical value because clinical phenotypes may overlap in the same patient and the same clinical phenotype could result from different biological mechanisms. With the goal of matching assessment to treatment choices, the most recent iteration of GOLD reorganized treatment objectives into two categories (improving symptoms, i.e., dyspnoea and health status, and decreasing future risk, as predicted by FEV1 level and exacerbations history), thus moving closer to individualized medicine using currently available bronchodilators and anti-inflammatory medications. Yet, future therapeutic options are likely to include targeting endotypes which reflect subtypes of patients defined by a distinct pathophysiological mechanism. Specific biomarkers of these endotypes would be particularly useful for clinical practice, especially when clinical phenotype alone is insufficient to identify the underlying endotype. Currently, a limited series of potential COPD endotypes and biomarkers have been suggested. We will gain empiric knowledge from proof of concept trials in COPD with emerging drugs that target specific inflammatory pathways. In each instance, specific endotyping and biomarker efforts will likely be required for success of these trials, since the pathways are likely to be operative in only a subset of patients. Network analysis of human diseases offers the possibility of a better understanding of disease patho-biologic complexity while facilitating the development of new therapeutic alternatives and, importantly, a reclassification of complex diseases. All these development should pave the way towards personalized treatment of COPD in the clinic.