Chlorophyll compounds and their derivatives containing metal or phytyl chain can be used as photosensitizer in photodynamic inactivation of microorganisms (PDI). So, the physicochemical properties and antimicrobial effect of chlorophyll derivatives were investigated: Mg-chlorophyll (Mg-Chl), Zn-chlorophyll (Zn-Chl), Zn-chlorophyllide (Zn-Chlde), Cu-chlorophyll (Cu-Chl), pheophytin (Pheo) and pheophorbide (Pheid). The photobleaching experiments showed photostability according to Cu-Chl > Pheo ∼ Pheid ≫ Zn-Chl ∼ Zn-Chlde > Mg-Chl. This order was discussed in terms of metal and the phytyl chain presences. Pheid and Zn-Chl in aqueous Tween 80 solution exhibited highest singlet oxygen yield compared with the other derivatives. Chlorophyll derivatives (CD) with phytyl chain was limited by the self-aggregation phenomenon at high concentrations, even in micellar systems (Tween 80 and P-123). The antimicrobial effect of CD derivatives was investigated against Staphylococcus aureus, Escherichia coli, Candida albicans and Artemia salina. Pheid showed the best results against all organisms tested, Zn-Chlde was an excellent bactericide in the dark and Cu-Chl had no PDI effect. No correlation with CD uptake by microorganisms and darkness cytotoxicity was found. The physicochemical properties allied to bioassays results indicate that Mg-Chl, Pheo, Zn-Chl and Pheid are good candidates for PDI.