Although there are several known methods by which to sample the upper and lower airways in asthmatic patients, new endpoints have emerged over the past few years from these sampling techniques that may be useful biomarkers. It is both timely and relevant that these endpoints be reviewed in the context of their role in asthma and hence as potential biomarkers in asthma. This article will cover various upper and lower airway sampling methods, and the standard and specialized endpoints that can be derived from those methods. For the nasal airways, this will include nasal lavage, exhaled nasal nitric oxide and acoustic rhinometry. For the lower airways this will include induced sputum, bronchoscopy-based methods and exhaled breath. Some methodologies such as bronchoscopy remain limited in their widespread clinical application due to their invasive nature. Less invasive techniques such as electronic nose and breath condensate have potential biomarker application but still require standardization and additional study. It is clear, however, that despite the applicability of a given sampling technique, both routine (cells and cytokines) and specialized (genomic, phenotypic, hydration) endpoints are measurable and should be combined in clinical trial studies to yield maximum results in asthma.