We use monodisperse poly(N-isopropylacrylamide) (PNIPAM) microgels as a model system for soft repulsive colloids and study their density dependent structural ordering and phase behaviour using confocal laser scanning microscopy (CLSM). The experiments are carried out at low temperatures, where the particles are in the swollen state and interact via a Hertzian potential, evidenced through a quantitative comparison of the pair correlation functions g(r) obtained with CLSM and computer simulations. We worked over a broad range of effective volume fractions ϕeff below and above close packing (ϕcp). CLSM allows us to identify a fluid–glass and a fluid–crystal transition by looking at the structure and dynamics of the suspensions. The density dependent g(r) values exhibit clearly visible anomalies at high ϕeff > ϕcp which we interpret as a structural signature of the glass transition related to the particle softness. These results are discussed in light of the previously studied phase behaviour of colloidal systems interacting with hard and soft repulsive interaction potentials.