The long-standing question of how asymmetric development or asymmetric body structures in lancelets (amphioxus) are phylogenetically related to the body plan of other animals is still untouched. Three anterior structures, the preoral pit, club-shaped gland and mouth, are remarkable asymmetric features in developing lancelets that all open on the left side of the body. A Ptx-related gene, BbPtx is the first identified transcription factor gene with an asymmetrical expression pattern in lancelets similar to that in vertebrates, and thus it may provide a clue for the above question. Expression of the BbPtx gene is first detected at the dorsal margin of the blastopore in early mid-gastrulae and then becomes restricted to the left anterodorsal wall of the primitive gut and to the developing left somitocoelomic system. Expression continues on the left side in the developing preoral pit, club-shaped gland and mouth as well as in the mesoderm at the caudal end. Unlike D-Ptx1 in Drosophila, BbPtx is not coexpressed with a fork head gene in lancelets; instead the two genes are expressed in a complementary fashion on the left side of the embryo. The expression pattern of BbPtx is not compatible with the calcichordate hypothesis of Jefferies, in which the proposed ancestor of chordates rotated its tail 90 degrees counterclockwise in relation to the head/trunk. The expression of both BbPtx and vertebrate Pitx2 in tissues derived from the coelom implies that the left-right asymmetric development has a common origin between cephalochordates and vertebrates. Considering the development of the coelom in deuterostomes, however, left-right asymmetric development involving Pitx2-related genes is rather likely to be a primitive character shared among deuterostomes.