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PurposeThe purpose of this paper is to present a localisation system for an indoor rotary‐wing micro aerial vehicle (MAV) that uses three onboard LEDs and base station mounted active vision unit.Design/methodology/approachA pair of blade mounted cyan LEDs and a tail mounted red LED are used as on‐board landmarks. A base station tracks the landmarks and estimates the pose of the MAV in real time by analysing images taken using an active vision unit. In each image, the ellipse formed by the cyan LEDs is used for 5 degree of freedom (DoF) pose estimation with yaw estimation from the red LED providing the 6th DoF.FindingsAbout 1‐3.5 per cent localisation error of the MAV at various ranges, rolls and angular speeds less than 45°/s relative to the base station at known location indicates that the MAV can be accurately localised at 9‐12 Hz in an indoor environment.Research limitations/implicationsLine‐of‐sight between the base station and MAV is necessary while limited accuracy is evident in yaw estimation at long distances. Additional yaw sensors and dynamic zoom are among future work.Practical implicationsProvided an unmanned ground vehicle (UGV) as the base station equipped with its own localisation sensor, the developed system encourages the use of autonomous indoor rotary‐wing MAVs in various robotics applications, such as urban search and rescue.Originality/valueThe most significant contribution of this paper is the innovative LED configuration allowing full 6 DoF pose estimation using three LEDs, one camera and no fixed infrastructure. The active vision unit enables a wide range of observable flight as the ellipse generated by the cyan LEDs is recognisable from almost any direction.