A method of manufacturing a cell structure, comprising: a step of adding a mixture of biocompatible macromolecular blocks, cells, and a liquid medium to a first culture container having a culture surface on which a plurality of recessed portions are formed and a side wall part standing on an outer periphery of the culture surface such that a liquid surface of the mixture is over the culture surface; a step of allowing a first culture container of the step to stand and forming a cell structure which includes the biocompatible macromolecular block and the cell in the recessed portion and in which the plurality of biocompatible macromolecular blocks are disposed in gaps between the plurality of cells; and a step of stirring and culturing a content of the first culture container obtained in the step in a second culture container comprising stirring means, (i) wherein the first culture container is allowed to stand in the step for a period of time for which a ratio of the number of cell structures manufactured after the step to the number of recessed portions is 70% or more, (ii) wherein the recessed portions are formed by 10 recessed portions/cm 2 to 10,000 recessed portions/cm 2 per unit area of the well forming area, and (iii) wherein the cells to be used are one or more selected from the group consisting of ES cells, iPS cells, MSCs, chondrocytes, osteoblasts, osteoprecursor cells, mesenchymal cells, myoblasts, cardiac muscle cells, cardiomyoblasts, nerve cells, hepatocytes, beta cells, fibroblasts, corneal endothelial cells, vascular endothelial cells, corneal epithelial cells, amniotic cells, umbilical cord blood cells, bone marrow derived cells, and hematopoietic stem cells. a step of adding a mixture of biocompatible macromolecular blocks, cells, and a liquid medium to a first culture container having a culture surface on which a plurality of recessed portions are formed and a side wall part standing on an outer periphery of the culture surface such that a liquid surface of the mixture is over the culture surface; a step of allowing a first culture container of the step to stand and forming a cell structure which includes the biocompatible macromolecular block and the cell in the recessed portion and in which the plurality of biocompatible macromolecular blocks are disposed in gaps between the plurality of cells; and a step of stirring and culturing a content of the first culture container obtained in the step in a second culture container comprising stirring means, (i) wherein the first culture container is allowed to stand in the step for a period of time for which a ratio of the number of cell structures manufactured after the step to the number of recessed portions is 70% or more, (ii) wherein the recessed portions are formed by 10 recessed portions/cm 2 to 10,000 recessed portions/cm 2 per unit area of the well forming area, and (iii) wherein the cells to be used are one or more selected from the group consisting of ES cells, iPS cells, MSCs, chondrocytes, osteoblasts, osteoprecursor cells, mesenchymal cells, myoblasts, cardiac muscle cells, cardiomyoblasts, nerve cells, hepatocytes, beta cells, fibroblasts, corneal endothelial cells, vascular endothelial cells, corneal epithelial cells, amniotic cells, umbilical cord blood cells, bone marrow derived cells, and hematopoietic stem cells. (i) wherein the first culture container is allowed to stand in the step for a period of time for which a ratio of the number of cell structures manufactured after the step to the number of recessed portions is 70% or more, (ii) wherein the recessed portions are formed by 10 recessed portions/cm 2 to 10,000 recessed portions/cm 2 per unit area of the well forming area, and (iii) wherein the cells to be used are one or more selected from the group consisting of ES cells, iPS cells, MSCs, chondrocytes, osteoblasts, osteoprecursor cells, mesenchymal cells, myoblasts, cardiac muscle cells, cardiomyoblasts, nerve cells, hepatocytes, beta cells, fibroblasts, corneal endothelial cells, vascular endothelial cells, corneal epithelial cells, amniotic cells, umbilical cord blood cells, bone marrow derived cells, and hematopoietic stem cells.