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Accurate temperature control with high spatial resolution is a challenging research topic in nano- and biotechnology. Due to their extraordinary physical and chemical properties carbon nanotubes reveal a promising potential as biomedical agents for temperature sensoring on the cellular level. Filling carbon nanotubes with tailored materials realises nanoscaled containers in which the active content is encapsulated by a protecting carbon shell. In particular, the filling with NMR active substances allows the usage as markers and temperature sensors. Their potential for biomedical applications is highlighted by temperature dependent NMR studies giving a proof-of-concept for a non-invasive temperature control on the cellular level.