Optical coherence tomography (OCT) is a non-invasive imaging method suited for probing translucent and semi-transparent samples. Based on the light backscattered from a sample, micrometer resolution imaging of tissue can be achieved in real-time. OCT has become a standard tool in clinical ophthalmology. It has greatly improved diagnosis and enabled precise and individual treatment planning of sight-threatening diseases such as age-related macular degeneration (AMD). Preclinical research in ophthalmology is essential for the basic understanding of diseases and is precious for fostering the development of new drugs targeting visual impairment. Histology is widely used for investigating the retina of animal models in preclinical research. Examination by histology provides sub-cellular resolution and numerous staining protocols allow a detailed analysis of the retina ex-vivo. However, preparation of tissue is cumbersome and longitudinal studies require a large number of animals. OCT was adapted for the eye of small animals and various works in literature have demonstrated the great potential of this technology for preclinical research. This thesis deals with functional extensions of OCT, which offer new contrast channels for intrinsic in-vivo "staining" of different retinal structures. In the first part of this work, a polarization-sensitive OCT system was utilized and augmented with OCT angiography to serve a multi-functional OCT system for small animal retinal imaging. A post-processing framework was implemented allowing efficient analysis of longitudinal OCT image data. In the first manuscript arising from this thesis, the framework itself is described along with the results of a longitudinal study spanning eleven months on the very low density lipoprotein receptor (VLDLR) knockout mouse model. These mutant mice develop retinal and choroidal neovascularization (NV) and are a popular model for AMD. Based on this first study, an advanced experiment with VLDLR knockout mice was conducted focusing on the early stage of spontaneous NV development and hence allowed a detailed staging of NV formation. Furthermore, an interventional study, where the eyes of VLDLR knockout mice were treated with aflibercept to inhibit NV development, was included. In a third study, intra-ocular pressure (IOP) increase was experimentally induced in the rat eye to model an acute glaucoma attack. Hereby, the effect of increased IOP on the pulsatility of the posterior rat eye was studied. A method was developed to assess tissue deformations between the retina and the chorio-scleral complex and fundus pulsations were mapped simultaneously with OCT angiography. The results presented in this thesis clearly demonstrate the suitability and versatility of OCT for longitudinal imaging of the rodent eye in preclinical studies.