This invention provides methods utilizing a microfluidic device that can quickly and accurately discern differences in deformability between individual cells and sets of cells and continuously fractionate populations of cells based on their deformability. This information may be important in disease diagnosis and treatment efficacy monitoring. For example such a device may be able to determine the stage of malarial infection by using red blood cell deformability. Additionally, methods of the invention may be used as a tool to screen drugs that can make cells more flexible in diseases such as sickle cell anemia that causes sickle cell crises. The relatively low manufacturing and operation costs of methods of the invention enable this device to be used in resource-limited settings to diagnose and monitor disease.