In the present thesis we demonstrate how under the appropriate dynamic control of light propagation, multimode fibers can be transformed into deterministic optical elements that along with their ultrathin size, large number of degrees of freedom and high Numerical Aperture, can be used as a new platform to fabricate miniature optical elements with applications in minimally invasive endoscopy, phototherapy and photoexcitation deep inside biological tissue. Firstly we demonstrate that using Digital Phase Conjugation, light can be focused into a diffraction limited spot at the output of a multimode fiber. The handling of the data in the digital domain, allows us to dynamically raster scan the focused spot across the whole fiber facet thus enabling the use of the system in scanning fluorescent imaging. We exploit the focusing and scanning capabilities of the system, along with the very small diameter of multimode fibers to demonstrate a rigid ultrathin high resolution endoscopic modality and perform fluorescence imaging of stained neuronal cells. The high quality of the obtained images allows the use of the system as a minimally invasive endoscope for cellular diagnosis via direct tissue penetration. Moreover, we extend the capabilities of the demonstrated device by performing imaging based on the optical absorption properties of samples via the photoacoustic effect. The use of a multimode fiber as the optical excitation part can enable the generation of new photoacoustic endoscopic modalities that can deliver optical resolution images deeper than the ballistic range of light propagation in tissue. Furthermore, we enhance the imaging capabilities of multimode fiber based imaging system by exploiting the properties of a highly scattering medium. The synergetic use of a multimode fiber and a scattering medium provides the imaging system with a higher number of degrees of freedom and enables the coupling of higher order to lower modes. Finally, aiming towards the fabrication of semi-flexible multimode fiber based endoscopic modalities, we demonstrate a system that is capable of overcoming the dependence of the modal mixing to the geometrical configuration of the fiber, to continuously focus through a bending multimode fiber. Overall, the presented results verify that the ultra-thin diameter of multimode fibers, in conjunction with the dynamic control of light transmission through them, allow us to envision multimode fibers as a new family of miniature versatile optical elements with multiple applications in biomedical optics.