A three-dimensional atom probe (3DAP) analysis is an efficient method in clarifying clustering behaviors of solute atoms. In this work, the shape and concentration of solute clusters in the early stage of low temperature aging were investigated for an Al–4.9mol%Zn alloy by the 3DAP analysis. The solute clusters in the alloy aged at 293 K were successfully detected and the growth behavior during aging was observed from the 3DAP maps. The shape of solute clusters depends on their sizes; i.e. the smaller clusters are in a spherical shape and the larger ones possess an ellipsoidal shape. Although larger solute clusters have a constant Zn concentration corresponding to the miscibility gap of GP zones, the solute concentration inside smaller solute clusters significantly varied.