Solid-state fermentation is an alternative culture method that has gained researchers attention over the past 20 years. There are several advantages in employing many SSF processes over the conventional submerged fermentation (SmF) ones, like higher yields of secondary metabolites or enzymes. Moreover, certain enzymes and secondary metabolites can only be produced in SSF. Many of these advantages are related to the special physiology shown by fungi in SSF. This review refers to this physiology (i.e. a behavior that deviates from the one displayed by the fungus in liquid medium), sometimes referred to as "physiology of solid medium", and its molecular basis. The reason for this different physiology in SSF is not fully understood, but recent advances are beginning to draw an interesting and wide panorama. Higher secondary metabolites production has been related to higher transcription of the biosynthetic genes: while studies on enzymes production in SSF have identified SSF-specific genes and provided deeper insight into their genetic expression and regulation. Moreover, some solid culture environmental stimuli (signals) have been identified. Many of these basic findings are also starting to be applied to new genetic improvement methods, novel culture systems, and other technological advances. (C) 2011 Elsevier Ltd. All rights reserved.