A sample preparation apparatus comprising: a storage container for containing liquid including a biological sample and a preservative solution; a filter for preventing a first cell in the biological sample from passing therethrough and that allows a second cell having a smaller diameter than that of the first cell to pass therethrough; a liquid separation section, to which the filter is provided, for separating, in the storage container and via the filter, the liquid into a first liquid mainly including the first cell and a second liquid mainly including the second cell; a disposal section for applying a negative pressure into the storage container so as to discharge the second liquid which has passed through the filter within the storage container, a substitution liquid supply section for supplying, into the storage container, a substitution liquid for substituting a part of the preservative solution in the storage container, a pressure-applying source for applying a positive pressure against the filter from an opposite side to a filtering area, such that the first cells clogging the filter are removed from said filter, and are floated into the first liquid remaining in a space between the filter and an interior surface of the storage container, and a liquid acquisition section for acquiring the first liquid separated by the liquid separation section remaining in the space between the filter and the interior surface of the storage container; and a sample preparation section for preparing a measurement sample from the first liquid acquired by the liquid acquisition section and a predetermined reagent, characterised in that: the sample preparation apparatus further comprises: a rotation member provided in the storage container for rotating in a direction along the filtering area of the filter having a contact with the liquid remaining in a space between the filter and the interior surface of the storage container. a storage container for containing liquid including a biological sample and a preservative solution; a filter for preventing a first cell in the biological sample from passing therethrough and that allows a second cell having a smaller diameter than that of the first cell to pass therethrough; a liquid separation section, to which the filter is provided, for separating, in the storage container and via the filter, the liquid into a first liquid mainly including the first cell and a second liquid mainly including the second cell; a disposal section for applying a negative pressure into the storage container so as to discharge the second liquid which has passed through the filter within the storage container, a substitution liquid supply section for supplying, into the storage container, a substitution liquid for substituting a part of the preservative solution in the storage container, a pressure-applying source for applying a positive pressure against the filter from an opposite side to a filtering area, such that the first cells clogging the filter are removed from said filter, and are floated into the first liquid remaining in a space between the filter and an interior surface of the storage container, and a liquid acquisition section for acquiring the first liquid separated by the liquid separation section remaining in the space between the filter and the interior surface of the storage container; and a sample preparation section for preparing a measurement sample from the first liquid acquired by the liquid acquisition section and a predetermined reagent, characterised in that: the sample preparation apparatus further comprises: a rotation member provided in the storage container for rotating in a direction along the filtering area of the filter having a contact with the liquid remaining in a space between the filter and the interior surface of the storage container.