An apparatus is provided with a cell culture container having a cell culture region made of a hole formed on a substrate, a semi-permeable membrane covering a top plane of the cell culture region and a culture medium replacement part provided over the semi-permeable membrane, a mechanism for supplying a cell culture medium into the cell culture container, and a microscopic optical mechanism for enabling long-term observation of the cell within the cell culture region. This apparatus makes it possible to culture a cell group originating from a particular single cell, to perform culture and observation while identifying cells to be subjected to interaction during the process of culturing cells, and observe a difference in variation between the particular cell and other cells. There is also provided a mechanism which makes it possible to collect only a cell assuming a particular state and perform analysis or biochemical measurement of a gene of the cell, an expressed mRNA and the like.