Earlier studies have shown that two types of septate junction are formed during early sea urchin morphogenesis. One type is the straight, unbranched, double septum septate (SUDS) which is found in the ectodermal layer throughout early development. The second type is formed only in cells which invaginate to become endoderm and to form the digestive tract. This junction is characterized by pleated, anastomosing, single septum septates (PASS). In order to ascertain in which parts of the digestive tract these junctions are formed, we studied exogastrulae because the endoderm is everted and forms constricted areas of the gut which are easily recognizable. Our results show that, in control embryos, SUDS septates are found in the mouth, esophagus and coelom and that PASS septates are found in the stomach, intestine and anus. These junctional types are also found in the same areas in exogastrulae; SUDS septates are found in the stomadeum, esophagus and coelom, and PASS septates are found in the stomach and intestine. The transition from SUDS to PASS junctions takes place within the same time period in exogastrulae as in normal embryos, i.e., from the time of mid-gastrulation through the pluteus stage. These results indicate that septate junction formation in the sea urchin embryo digestive tract may be genetically programmed in terms of both time and spatial location. This program is not altered either by the major dislocation of cells from their normal position within the embryo or from normal contacts with neighboring cells.