Osteochondral tissue repair represents a common clinical need, with multiple approaches in tissue engineering and regenerative medicine being investigated for the repair of defects of articular cartilage and subchondral bone. A full thickness rabbit femoral condyle defect is a clinically relevant model of an articulating and load bearing joint surface for the investigation of osteochondral tissue repair by various cell-, biomolecule-, and biomaterial-based implants. In this protocol, we describe the methodology and 1.5- to 2-h surgical procedure for the generation of a reproducible, full thickness defect for construct implantation in the rabbit medial femoral condyle. Furthermore, we describe a step-by-step procedure for osteochondral tissue collection and the assessment of tissue formation using standardized histological, radiological, mechanical, and biochemical analytical techniques. This protocol illustrates the critical steps for reproducibility and minimally invasive surgery as well as applications to evaluate the efficacy of cartilage and bone tissue engineering implants, with emphasis on the usage of histological and radiological measures of tissue growth. Impact statement Although multiple surgical techniques have been developed for the treatment of osteochondral defects, repairing the tissues to their original state remains an unmet need. Such limitations have thus prompted the development of various constructs for osteochondral tissue regeneration. An in vivo model that is both clinically relevant and economically practical is necessary to evaluate the efficacy of different tissue engineered constructs. In this article, we present a full thickness rabbit femoral condyle defect model and describe the analytical techniques to assess the regeneration of osteochondral tissue.