Antimicrobial activity and antibiotic susceptibility were tested for 23 Lactobacillus and three Bifidobacterium strains isolated from different ecological niches. Agar-well diffusion method was used to test the antagonistic effect (against Staphylococcus aureus, Escherichia coli, Bacillus cereus and Candida albicans) of acid and neutralized (pH 5.5) lyophilized concentrated supernatants (cell-free supernatant; CFS) and whey (cell-free whey fractions; CFW) from de Man-Rogosa-Sharpe/trypticase-phytone-yeast broth and skim milk. Acid CFS and CFW showed high acidification rate-dependent bacterial inhibition; five strains were active against C. albicans. Neutralized CFS/CFW assays showed six strains active against S. aureus (L. acidophilus L-1, L. brevis 1, L. fermentum 1, B. animalis subsp. lactis L-3), E. coli (L. bulgaricus 6) or B. cereus (L. plantarum 24-4В). Inhibition of two pathogens with neutralized CFS (L. bulgaricus 6, L. helveticus 3, L. plantarum 24-2L, L. fermentum 1)/CFW (L. plantarum 24-5D, L. plantarum 24-4В) was detected. Some strains maintained activity after pH neutralization, indicating presence of active substances. The antibiotics minimum inhibitory concentrations (MICs) were determined by the Epsilometer test method. All strains were susceptible to ampicillin, gentamicin, erythromycin and tetracycline. Four lactobacilli were resistant to one antibiotic (L. rhamnosus Lio 1 to streptomycin) or two antibiotics (L. acidophilus L-1 and L. brevis 1 to kanamycin and clindamycin; L. casei L-4 to clindamycin and chloramphenicol). Vancomycin MICs > 256 μg/mL indicated intrinsic resistance for all heterofermentative lactobacilli. The antimicrobially active strains do not cause concerns about antibiotic resistance transfer and could be used as natural biopreservatives in food and therapeutic formulations.