Providing a method of estimating the number of microparticles such as microorganisms in a sample, without performing complicated operations. The method comprises counting by constant flow the number of target microorganisms contained in the sample at a predetermined flow rate, sectioning measurement data obtained as a result of the constant flow counting into a predetermined number of sections by a predetermined unit time for a section, counting the number of sections in which microorganisms are detected and the number of sections in which they are not detected, in the predetermined number of sections; and estimating the number of microorganisms in the sample, by a statistical method from the flow rate of the sample in the constant flow counting step, the predetermined number of sections and the predetermined unit time in the sectioning step, and the number of sections in which microorganisms are detected in the counting step.