Nanocrystalline chlorapatites (Ca10(PO4)6Cl2) doped with lanthanide ions (Eu3+, Er3+ and Yb3+) and co-doped with silver ions (Ag+) were synthesized by a hydrothermal synthesis route. XRD, TEM, and SAED measurements indicated that the powders are single phased and crystallize with a hexagonal structure with good dispersion. The results showed well crystallized chlorapatite grains with a diameter of about 45 nm. The antimicrobial activity of the nanoparticles against Escherichia coli ATCC 11229 and ATCC 25922, Klebsiella pneumoniae ATCC 700603, and Pseudomonas aeruginosa PAO1 and ATCC 27853 was studied. The best activity was observed for the Eu3+,Ag+:Ca10(PO4)6Cl2 and Eu3+,Ag+,Yb3+:Ca10(PO4)6Cl2 compositions. These multifunctional nanocrystalline powders could be used as a promising antimicrobial agent and material for bio-detection.