Skin grafts were performed to prove the level of genetic diversity in chicken populations of the Obese strain (OS), which develops a spontaneous Hashimoto's-like thyroiditis, and University of California at Davis (UCD) Line-200 chickens, which are hereditarily afflicted with progressive systemic sclerosis (scleroderma). As controls, Cornell C-strain (CS) and inbred, normal White Leghorn CB chickens were included in the genetic monitoring program. At the commencement of this study in 1988, median allograft rejections were observed after 9 to 12 d (range 8 to 14 d) in OS and CS chickens that derived from large flocks at Cornell University, whereas OS sublines of the smaller, more closely-bred colonies at the University of Innsbruck, Austria, showed median allograft rejection after 19 d (range 12 to 35 d). From 1988 to 1993, allograft survival was only slightly prolonged in the OS sublines. However, the results of the skin allotransplantations in inbred UCD-200 chickens revealed two subpopulations in this line. In one subgroup the median of allograft rejection was calculated with 13 d (range 6 to 37 d) in 1989, 30 d (10 to 37 d) in 1990, 21 d (8 to 90 d) in 1991, and 16 d (7 to 26 d) in 1993. In the other subgroup allografts were accepted at rates similar to autografts. In addition, the inbreeding coefficient was calculated for eight male and eight female OSB5B5Cornell (C) and OSB5B5Innsbruck (INN) chickens, respectively, hatched in 1993. On the basis of mating records, the minimal estimate of the inbreeding coefficient was calculated to be 0.0679 in the OSB5B5C and 0.1035 in the OSB5B5INN population. The results demonstrated a higher degree of consanguinity in the smaller population of OSB5B5INN chickens compared to OSB5B5C birds. The later are maintained in larger numbers, therefore, the frequency of matings between related individuals should be lower.