A general-purpose software package, termed DE Novo OPTimization of In/organic Molecules (DENOPTIM), for de novo design and virtual screening of functional molecules is described. Molecules of any element and kind, including metastable species and transition states, are handled as chemical objects that go beyond valence-rules representations. Synthetic accessibility of the generated molecules is ensured via detailed control of the kinds of bonds that are allowed to form in the automated molecular building process. DENOPTIM contains a combinatorial explorer for screening and a genetic algorithm for global optimization of user-defined properties. Estimates of these properties may be obtained to form the fitness function (figure of merit or scoring function) from external molecular modeling programs via shell scripts. Examples of a range of different fitness functions and DENOPTIM applications, including an easy-to-do test case, are described. DENOPTIM is available as Open Source from https://github.com/denoptim-project/DENOPTIM .