Embryos develop to adults through a complicated process of cell division and migration, i.e., morphogenesis. Not only biochemical factors but also mechanical factors such as stress and stiffness should be involved in morphogenesis because cells move vigorously while pushing and pulling each other. Such pushing and pulling may cause complicated distribution of residual stress in the embryo. Residual stress of an elastic body can be estimated by measuring surface topography of a cross-section of the body because the area subjected to tensile stress dents and the area subjected to compressive stress bulges in the section. In this study, we estimated stress distribution in Xenopus laevis embryo during the gastrula stage (stages 10-13), where a hollow ball-like structure transforms into a complicated three-layered structure (endoderm, mesoderm and ectoderm) with a part of the outside wall of the embryo entering the embryo's interior, by measuring the surface topographies of the median section and a section perpendicular to the median plane and containing a dorsal marginal zone (DMZ). We found that 1) ectoderm was in tension whereas meso-endoderm in compression, 2) the magnitude of the stress decreased during stages 11 and 12, and 3) the stress was higher in the DMZ than in surrounding areas at stage 10.