Methods and compositions are provided for the treatment and repair of defect in the cartilage in partial- or full-thickness defects in joints of animals, in particular humans. To induce cartilage formation, a defect in cartilage is filled with layers of thin flaps of synovium or of peritendineum, which contains chondro- and osteo-progenitor cells, with interposed layers of a matrix. The matrix contains a chondrogenic factor, which induces chondrogenesis of chondroprogenitor cells in the flaps, and an anti-hypertrophic agent, which arrest differentiation of chondrocytes in an early phase, in an appropriate delivery system. The matrix filling the bone area of a full-thickness defect may contain an osteogenic factor, which induces osteogenesis of osteoprogenitor cells. The layer of a flap between cartilage and bone areas may work as a barrier, which prevents blood vessels and associated cells from penetrating from the bone area into the cartilage area. To promote the induction of chondro- and osteo-genesis of the progenitor cells in the flaps of synovium or peritendineum effectively, the flaps may be treated with enzymes, e.g., matrix metalloproteinases or be punched by a needle before filling a defect.