In this study it is described beads based isolation assay terminated by electrochemical analysis of hemagglutinin (HA) using two different cadmium quantum dots (QDs) labelled as CdS and CdTe. The two steps assay was suggested as the first step was the automatic isolation of HA labelled by Cd QDs using glycan modified paramagnetic particles (MPs), and the second one was the electrochemical detection of HA-QDs complex by voltammetry, particularly, adsorptive transfer technique coupled with differential pulse voltammetry Brdicka reaction was used for detection of HA and differential pulse anodic stripping voltammetry was used for detection of Cd. Both methods were optimized. Suggested assay can be used for the subtyping and quantification of HA.