A cell processing apparatus includes a storage container that contains liquid L including a biological sample; a filter that prevents a first cell C1 in the biological sample from passing and allows a second cell C2 having a smaller diameter than that of the first cell C1 to pass; and a filtration cylinder for separating, in the storage container and via the filter, the liquid L into a first liquid L1 mainly including the first cell C1 and a second liquid L2 mainly including the second cell C2. A measurement target cell filtered by the filter among other cells can be easily collected.