Hydroxyapatite (HA) nanoparticles with homogeneous rod morphology were successfully synthesized by the hydrothermal method. The use of cationic and anionic surfactants (cetyltrimethylammonium bromide, CTAB, and sodium dodecyl sulfate, SDS) does not change the morphology, but the length/diameter ratio of HA nanorods did. The structural characterizations revealed well-crystallized samples in the hexagonal phase. The HA samples with a smaller Ca/P ratio presented larger crystalline size. The CTAB- sample present antibacterial activity against Pseudomonas aeruginosa, Escherichia coli, Streptococcus anginosus, Staphylococcus aureus, Micrococcus luteus, and Klebsiella pneumoniae suggesting that the bacteria nature and surface charge of nanoparticles affect the susceptibility.