A two-stage pulse tube refrigerator having a compact design, low vibration and low heat loss is provided where at least the 2nd stage is co-axial but preferably, both stages are co-axial with the second stage pulse tube being central and the first stage pulse tube occupying the annular space between the second stage pulse tube and the first stage regenerator. Convection losses associated with different temperature profiles in the pulse tubes and regenerators are minimized by shifting the thermal patterns in the pulse tubes relative to the regenerators by one or more of spacers in the regenerators, physical differences in length with gas channel connections, adjustment of dc flow, and thermal bridges.