Magnetic nanoparticles (MNPs) are allowing for new approaches to drug delivery, biomarker capture and are also enabling cancer treatments such as magnetic field hyperthermia and magnetic drug delivery. Applied research into functionalised MNPs is now advancing to in-vivo studies as their unique properties such as magnetic responsiveness and small scale are being exploited to overcome some pre-existing limitations for non-invasive in-vivo applications. One prominent application is magnetophoretic delivery of MNPs within tissue to a desired location in the body. While there has been an increasing interest in magnetophoresis from a fundamental point of view, a detailed picture of how the motion of MNPs is influenced by the characteristics of the surrounding tissue environment is lacking. Addressing this would improve reliability, accuracy and precision of magnetic guidance techniques. By understanding how molecular interactions influence functionalised MNPs interactions with biological tissue, appropriate measures can be taken in their future design and in-vivo delivery to ensure precise and reliable magnetic motion and guidance. This thesis attempts to contribute to the understanding of magnetophoretic behaviour of functionalised iron oxide nanoparticles in biological tissue. In the first instance, a new optical imaging method is proposed to study functionalised MNPs undergoing magnetophoretic transport through biological tissue mimics including hydrogels and cultured extracellular matrix (ECM). Following the establishment of the method, the impact of chemical and physical attributes of the MNP, as well as the nature of the tissue mimic environment and their interactions, on magnetophoretic motion in different field gradients is examined. This work provides insights into electrostatic interactions as a modulator of magnetophoretic transport of MNPs which are important in the context of biological transport, given the nature of the ECM in tissue. The application of this new knowledge is then applied to biomarker sampling from tissue mimics using functionalised MNPs. The impact of MNP-biomarker binding and uptake on magnetophoretic behaviour is investigated and the analytical capability of the novel approach elucidated. The approach developed here is demonstrated to have potential for minimally-invasive sampling of biomarkers from complex, biphasic environments such as the ECM.