The successful treatment of maladies like cancer via photodynamic therapy during the last 40 years suggested photodynamic inactivation (PDI) of micro-organisms to be an application with high potential to overcome the problems of resistances and toxicity of antibiotics and biocides. Yet from the high diversity of medically and environmentally relevant micro-organisms new demands arose concerning composition of photosensitizers and modes of application, initiating widespread research with increasing cases of multiresistant bacteria worldwide. After two decades it only just became possible to photodynamically inhibit phototrophic micro-organisms as well as mold fungi in addition to yeasts, gram positive and negative bacteria. This chapter gives an overview over the extensive research and clinical studies on PDI of bacterial and fungal infections. Furthermore, the latest achievements on the relatively new subject of photodynamic inactivation of relevant environmental micro-organisms like mold fungi and phototrophic micro-organisms are presented.