Understanding of the roughness-induced laminar–turbulent transition of supersonic and hypersonic flows is partly challenged by the intricate sensitivities presented by different correlation criteria. We investigate experimentally the effect of height for an isolated roughness element of quadrilateral planform. Heat transfer measurements document the enhancement of roughness-induced disturbances – here the associated heat flux perturbation – along a downstream axisymmetric laminar separation. With increasing element height , a gradual intensification in wake disturbance levels is found for subcritical elements ( , where is the undisturbed boundary layer thickness) while elements taller than the effective condition ( ) bypass the more moderate transition mechanisms to produce a fully turbulent element wake. Results exhibit high sensitivity to flow properties at roughness height between critical and effective conditions. A reduction in wake disturbance levels with increasing height is documented within . This effect coincides with a decrease in kinematic viscosity at roughness height (as Mach number at height increases from 1.52 to 1.96) and is restricted to elements with strong local separation, whereby the influence of local shear effects is enhanced.