We propose a procedure to reconstruct characteristic features of an unknown stochastic system from the long-time full counting statistics of some of the system's transitions that are monitored by a detector. The full counting statistics is conveniently parametrized by so-called generalized factorial cumulants. Taking only a few of them as input information is sufficient to reconstruct important features such as the lower bound of the system dimension and the full spectrum of relaxation rates. The use of generalized factorial cumulants reveals system dimensions and rates that are hidden for ordinary cumulants. We illustrate the inverse counting-statistics procedure for two model systems: a single-level quantum dot in a Zeeman field and a single-electron box subjected to sequential and Andreev tunneling.