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Mice that are double heterozygous for the semi-identical T(1;13)70H and T(1;13)1Wa reciprocal translocations display a great variation in male fertility. The synaptic behaviour of the different translocation chromosomes of adult males was studied in relation to this parameter. Juvenile males and embryonic females (16 and 18 days old) were included for comparison. In agreement with the minor differences in the translocation breakpoint positions, two differently sized heteromorphic bivalents are formed in meiotic prophase of both sexes (a quadrivalent was never encountered). Synaptonemal complex (SC) configurations of both bivalents in either sex are characterized by a high degree of non-homologous synapsis at zygotene-early pachytene. The rate of synaptic adjustment during pachytene is dependent on the size of the heteromorphic bivalent and varies between the sexes. Differences in SC configuration and morphology of the small heteromorphic bivalent in particular exist between the sexes and between animals. In males, this correlates with different degrees of fertility. Normal SC morphology in a fully synapsed small heteromorphic bivalent is an important determinant of successful meiosis and spermatogenesis. Moreover, aberrant synapsis favours the ‘unsaturated pairing site’ model as the primary cause for male sterility.