Heritable mutations in the germ line lead to genetically heterogeneous, or mosaic, gonads. Many of the genes used in germ-line development also play roles in somatic development [Saffman, E. E. & Lasko, P. (1999) Cell. Mol. Life Sci. 55, 1141-1163]. Mutations in these genes may have cellular phenotypes throughout germ-line development leading to their differential elimination or survival, as has been observed in somatic cells [Morata, G. & Ripoll, P. (1975) Dev. Biol. 42, 211-221]. We investigate whether mutations in heterozygosis are subject to pregametic selection in the germ line. We initiated clones of wild-type homozygous cells at different stages of development in gonads heterozygous for eight different recessive chromosome deficiencies. Here we show that cell selection takes place in mosaic germ-line populations. This phenomenon represents a level of selection that precedes and conditions subsequent zygotic selection by affecting the genes available in the gametic population.