The hierarchical structure of scale-free networks has been investigated focusing on the scaling of the number N(h)(t) of loops of size h as a function of the system size. In particular, we have found the analytic expression for the scaling of N(h)(t) in the Barabási-Albert (BA) scale-free network. We have performed numerical simulations on the scaling law for N(h)(t) in the BA network and in other growing scale-free networks, such as the bosonic network and the aging nodes network. We show that in the bosonic network and in the aging node network the phase transitions in the topology of the network are accompained by a change in the scaling of the number of loops with the system size.