This study evaluated microscopic flaws in the healing rabbit medial collateral ligament and their significance in terms of the material properties of this ligament during healing. A gap injury was created in the midsubstance of the medial collateral ligament in the right hindlimb of 15 skeletally mature (12 months old) New Zealand White rabbits. At postoperative intervals of 3, 6, or 14 weeks, histomorphometric analysis of the flaws was carried out in subgroups of animals. The medial collateral ligaments from four of the left hindlimbs (randomly selected) were used as uninjured contralateral controls. In one histologic section of each area of scar tissue and the analogous area in the controls, specified tissue flaws (blood vessels, fat cells, hypercellular areas, loose matrix, disorganized matrix, or a combination of these) were measured by four independent and blinded observers. The results showed that the mean total area of the flaws, as a percentage of the total section, and the mean area of the largest flaw decreased with healing time in each healing group but did not achieve control values by 14 weeks. Because it was not possible to test the healing medial collateral ligaments mechanically prior to measurement of the flaws (due to the destructive nature of failure testing), the data on the flaws were compared with the material strength and stiffness of a separate series of similarly injured and mechanically tested medial collateral ligaments (data published previously). A maximum likelihood statistical analysis showed a very strong functional association between the mean area of the largest flaw and the stress at failure (p < 0.004) and between the mean flaw area as a percentage of the total section area and the elastic modulus (p < 0.001). This study therefore demonstrates that it is possible to quantify material flaws in scar tissue in rabbit medial collateral ligaments, that these flaws become smaller with healing time as the scar remodels, and that flaws are functionally associated with the material properties of the ligament in this model (larger flaws with less tensile strength and more flaws with less stiffness).