The secondary flows of different types were studied in a boundary layer of cyclonic vortex over localized heater. Near the periphery of the heating area system of horizontal rolls oriented along the basic flow is formed. Thermal plumes which are originated between counter-rotating horizontal rolls are pushed to the centre by basic flow and create spiral bands. Both types of observed secondary flows (rolls and spiral bands) are of convective nature. Cyclonic vortex becomes unstable at low values of viscosity and fast rotation of the experimental model. The instability of the vortex is tightly connected with a structure of the radial inflow. For moderate values of rotational Reynolds number Re the radial flows consist of several branches which transport angular momentum to the centre of the model. When Re exceeds critical value (about 23) radial inflow changes its structure and appears as one wide branch which does not reach the centre. As a result the vortex that slowly moves around the centre is formed instead of the vortex localized in the centre. Further increase of Re leads to chaotic state with several vortices which appears at different locations near the periphery of the heating area. The map of regimes with stable and unstable vortices is presented. The applicability of experimental results to the formation of large-scale atmospheric vortices is discussed.