Detecting life-threatening diseases is a major challenge in biomedicine, as it requires pathogen identication on the molecular level. One promising detection strategy relies on attaching molecular probes to nanoparticles (NPs), which support localised surface plasmon resonance (LSPR). Probe-functionalised NPs can then detect molecular DNA-binding events via a macroscopic change in their optical response. Until now, NP-sensing schemes have been primarily implemented using planar substrates, requiring complex launching techniques and cost-intensive microscopy. An alternative approach adopted in this work involves inltrating optical bres with NPs allowing LSPR excitation and spectral multiplexing within one device. The principle idea relies on probing deposited plasmonic NPs by propagating optical fibre modes, leading to hybrid plasmonic-photonic fibres for biosensing. An important class of innovative bres exploited in this work are microstructured optical bres (MOFs) containing longitudinally invariant microstructures. These structures enable unprecedented adjustment of light matter interaction resulting in a high degree of sensitivity and an optofluidic environment ideally suited for biochemical application. In this thesis optofluidic channels are integrated in direct proximity to the light guiding core, boosting the light-analyte interaction length by orders of magnitude. This concept thus represents a multiscale approach, fundamentally connecting the microscopic level via LSPR-mediated sensing with the macroscopic world using MOFs leading to a novel and unexplored sensor platform. This study shows that combining plasmonic-bre waveguides with microuidics yields a highly integrated, reusable, optouidic interface for efcient refractive index sensing with outlook for DNA diagnostics. This unique combination is extremely attractive from both device and clinical point of view, as the flexible handling of optical fibres principally enables in-vivo application.