In order to improve poly(lactic acid) (PLA) mechanical, thermal, and barrier properties, different layered silicate nanoclays are added. This work deals with the study of the effect of the type of nanoclays with different hydrophilicity on the preparation procedure and properties of PLA nanocomposites. Six kinds of clays have been loaded in PLA whose hydrophilicity varies in the following order of increased hydrophilicity: modified Dellite 67G (67G) < Cloisite 15A (C15A) < C20A < C93A < C30B < hydrophilic smectite clay (HPS). Resultant nanocomposites have been characterized both with respect to bulk and surface properties by mechanical, rheological, thermal analyses, X-ray diffraction study, Fourier transform infrared spectroscopy, gas permeability tests, contact angle measurements, scanning electron microscopy, and atomic force microscopy. Antimicrobial properties have been also tested. Evidenced was the dependence of most properties on the hydrophilicity/hydrophobicity of the clays. The nanocomposites containing the most hydrophilic clays such as Cloisite 93A, Cloisite 30B, and HPS show satisfactory antimicrobial activity against both Gram-positive and Gram-negative bacteria, excepting fungus Candida albicans.