Adult Drosophila mosaics can be used to study cell lineage and to map relative positions of primordia at the blastoderm stage. This information can define which germ layer an organ comes from and can help build models of genetic regulation of development. Here we use the sdh cell marker to map internal organs in mosaics made by nuclear transplantation. We confirm that oenocytes arise from the same progenitors as the adult epidermis, but that muscles and fat body have a separate (mesodermal) origin and that the precursors of epidermis and central neurones are closely intermingled in the ventral, but not dorsal, epidermis. We find that the malpighian tubules are more closely related to the hindgut than the midgut and are therefore ectodermal in origin. We find that each intersegmental muscle in the thorax arises from one specific parasegment in the embryo, but that very small numbers of myoblasts wander and contribute to muscles of inappropriate segments. We present evidence indicating that the visceral muscles of the midgut have a widely dispersed origin (over much of the embryo) while the somatic mesoderm of the female gonad comes from a small number of abdominal segments. The visceral mesoderm of the hindgut develops from a localized posterior region of the embryo.