The use of carbon nanotubes in medicine is now at the crossroads between a proof-of-principle concept and an established preclinical candidate for a variety of therapeutic and diagnostic applications. Progress towards clinical trials will depend on the outcomes of efficacy and toxicology studies, which will provide the necessary risk-to-benefit assessments for carbon-nanotube-based materials. Here we focus on carbon nanotubes that have been studied in preclinical animal models, and draw attention to the promises, facts and challenges of these materials as they transition from research to the clinical phase. We address common questions regarding the use of carbon nanotubes in disease imaging and therapy, and highlight the opportunities and challenges ahead.