High sensitivity, selectivity, and stability are key requirements for carbon nanotube (CNT)-based sensors to realize their full potential in applications ranging from chemical warfare agent detection to disease diagnostics. Herein we demonstrate the sensing of volatile organic compounds (VOCs) relevant to human diseases using an array of chemiresistive carbon nanotube (CNT)-based sensors functionalized with ionic liquids (ILs). The ILs are fluid at ambient temperature and were selected to produce a discriminating sensor array capable of the gas-phase detection of human disease-related VOCs. We find that sensor arrays consisting of imidazolium-based ILs with different substituents and counterions provide selective responses for known biomarkers of infectious diseases of the lungs. Specifically, the sensors discriminate the various volatile biomarkers for tuberculosis based on their polarity, solubility, and chemical affinities. In addition to selectivity, the sensors also show a high level of reversibility and promising long-term stability, which renders them to be suitable candidates for practical applications in breath analysis.