Novel biomedical composites, based on organically modified vermiculite and montmorillonite with deposited Ca-deficient hydroxyapatite (CDH), were prepared. The monoionic sodium forms of vermiculite and montmorillonite were intercalated with chlorhexidine diacetate (CA). The surfaces of organoclays were used for the precipitation of Ca-deficient hydroxyapatite. The composites with Ca-deficient hydroxyapatite showed very good antibacterial effects, similar to the antimicrobial activity of pure organoclay samples. Better antibacterial activity was shown in the organically modified montmorillonite sample with Ca-deficient hydroxyapatite compared with the vermiculite composite, but, in the case of Staphylococcus aureus, both composites showed the same minimum inhibitory concentration (MIC) value. The antimicrobial effect of composites against bacteria and fungi increased with the time of exposure. The structural characterization of all the prepared materials, performed using X-ray diffraction and FT infrared spectroscopy analysis, detected no changes in the original clay or CDH during the intercalation or precipitation process, therefore we expect the strength of the compounds to be in the original power.