A method and system for performing mixing in a low volume, low aspect ratio microfluidic chamber (3) is described. Two or more mixing bladders (13,15) formed adjacent the microfluidic chamber are inflated and deflated in reciprocating fashion to cause inward and outward deflection of discrete regions of the chamber wall to mix fluid within the chamber. Mixing bladders are actuated by air or another gas, or by a liquid such as water, pumped in and out of the bladders with a pump which may be located remote from the microfluidic device including the microfluidic chamber. In an alternative embodiment, mixing is generated by applying alternating mechanical forces to a surface of a flexible chamber forming device. The microfluidic chamber may be a hybridization chamber formed on a microarray (25) slide with the use of a microarray interface device, or it may be a microfluidic chamber formed in various other types of microfluidic devices.