Although there is increasing interest in using pulmonary biomarkers for a more complete and clinically relevant assessment of COPD and a plethora of biomarkers are becoming available, there is little information regarding their reproducibility and correlation with other outcome measurements in COPD. The lack of well-validated biomarkers that can be used for monitoring disease activity, predicting future clinical outcomes and the effect of therapeutic interventions highlights the factual need to identify new biomarkers in COPD. It is likely that, using what is called 'integrative functional informatics', which is a novel direction in the interfacing and integration of different technologies (genomics, proteomics, metabolomics and metabonomics, pharmacogenetics, and integrative approaches) for collection and analysis of data on biomarkers, we will be able to identify robust, reliable, and reproducible biomarkers in COPD.