The present invention provides a cleaning method by which the performance of a microchip can be recovered and a cleaning liquid. A method for cleaning a microfluidic device comprising: cleaning a channel that is formed in the microfluidic device, has a surface having a polymer coating, and has been brought into contact with a sample containing nucleic acid and/or protein, by bringing the channel into contact with a cleaning liquid comprised only of an organic solvent having solubility in at least the same volume of water at 25° C., or a cleaning liquid containing 50 vol % or more of the organic solvent in a buffer solution. The method wherein the buffer solution has a pH of 8 to 10. The method wherein the buffer solution further contains 3 to 8M of a protein denaturant. The method wherein the buffer solution has a pH of 2 to 4.