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Osteochondral transplantation requires a careful assessment of the location of donor plugs. A mismatch of cartilage thickness between the donor and recipient site may lead to abnormal stresses and poor function. The objective of this study was to characterize the recommanded donor and recipient sites with respect to cartilage thickness in younger individuals. Nineteen arthro CT (13 men, 6 women), which had been carried out in a population of less than 50 years old were studied. Recommanded donor sites have included the posterior femoral condyles, the medial and lateral aspect of the trochlea and central, medial and lateral sides of the intercondylar notch. Recipient sites were studied at four regions of interest on the medial femoral condyle usually involved in osteochondritis dissecans. Average cartilage thickness was calculated on the digital version of the reference cuts for each site and compared. The sensitivity of the precision of the measurements to observer variability was evaluated using intra- and inter-observer correlation coefficient tests. The femoral cartilage in the knee was thickest in the recipient sites (2.49 mm, SD 0.64) than in donor sites (1.79 mm, SD 0.43) (P < 0.0001). There was no differences between the different donor sites, unless for the antero lateral intercondylar notch which was significantly thinner (1.3 mm, SD 0.29) than the other sites (P < 0.05). The cartilage of the donor site was consistently thinner than the cartilage of the recipient sites. Between the different donor sites, the lateral side of the intercondylar notch was significantly thinner than the other donor sites and should not be harvested in priority.