In the current review we summarised the research involving solid state fermentation (SSF) for the production of compounds that could be used in healthcare (terpenoids, polyphenols, fibrinolytic enzymes, mycophenolic acid and others). We described several groups of obtained agents which hold various activity: antimicrobial, anti-inflammatory, immunosuppressive, anticoagulant and others (e.g. anticancer or anti-diabetic). It seems that especially terpenoids and polyphenols could be useful in that field, however, other substances such as enzymes and fatty acids play important role as well. We described main groups of microorganisms that are applied in SSF of those compounds, particularly Bacillus genus and fungi, and where possible provided information regarding genes involved in those processes. We also compared various approaches toward optimisation of SSF.