Experimental and analytical tools will be developed to detect and characterize exoplanetary atmospheres during transits. Particular attention will be paid to HD 209458B (for which only atomic species have been observed to date) and the detection of infrared H3 molecular absorption lines using high resolution high signal-to-noise near infrared spectroscopy. As one of the dominant regulators of thermal balance in gas giant ionospheres, this molecule is of interest as a diagnostic of the atmospheric interface and will yield valuable information on the thermodynamic conditions in the outer atmosphere. Analysis and statistical modeling of molecular absorption lines of H3 will enable a direct probe of the temperature, column density and structure of the thermosphere of Hot Jupiters and constrain current models. To meet the project goals, sophisticated data reduction and analysis methods will also be formulated and employed. The work here will provide input into the design and development of future instruments for the detection of molecular absorption in exoplanetary atmospheres. The algorithms developed here will also be made publicly available. Graduate students and undergraduates (through the NSF sponsored Research Experiences for Undergraduates at Notre Dame) will play a significant role in the research and subsequent dissemination.