A survey of consanguineous marriages in Japan was conducted on 1 September 1983, by questionnaires. The total number of couples surveyed was 9225. They were chosen from six widely different areas and the inbreeding coefficients from isonymy and pedigrees were estimated for each area. Random inbreeding remained constant with the marriage year whereas total (F) and non-random (Fn) inbreeding from isonymy and inbreeding from pedigrees (α) decreased with the marriage year in each area. Estimates of genetic microdifferentiation from surnames were obtained; estimates of the reduced variance indicated low microdifferentiation (0·000014-0·000081) in five areas and a higher value in Fukue City (0·0004). The ratio of FST (the average within-group a priori kinship) to α-value ranged from 0·42 in Kawanishi City to 3·9 in Minobu-Cho.