This study was performed to identify various bacteria from feces of calves suffering from diarrhea, and to determine in vitro antimicrobial activity of silver, gold and copper nanoparticles against the antibiotic-resistant bacteria isolated from fecal samples. Fecal samples were collected from 153 diarrheic calves and primarily tested for the presence of Escherichia coli, Salmonella spp. and Staphylococcus aureus using bacteriological examination, biochemical reactions and polymerase chain reaction. The minimum inhibitory concentrations of silver, gold and copper nanoparticles against identified bacterial isolates were determined by a broth dilution method. 84 bacterial isolates from the 153 fecal samples were identified using bacteriological, biochemical and genotypical methods. Escherichia coli was considered the most frequent bacterium isolated numbering 31 (36.90%) followed by Salmonella sp. as the second most prevalent 16 (19.04%). Further isolates such as Staphylococcus aureus 10 (11.90%) were isolated and identified. The MIC values of silver, gold and copper nanoparticles with a size of 10 nanometers (nm) against the three types of bacteria were ranged from 0.625 to 10 μg/ml, 2.5 to 20 μg/ml and 2.5 to 20 μg/ml, respectively. While these values with a size of 20 nm were 0.312 to 2.5 μg/ml, 1.25 to 10 μg/ml and 2.5 to 10 μg/ml, respectively. Additionally, the mean time of the antimicrobial action of silver, gold and copper nanoparticles at concentration 10 nm against all isolates was 5 min, 30 min and 15 min, respectively. Using of these nanoparticles in a concentration of 20 nm, the mean time was 1, 15 and 5 min, respectively. These in vitro results clearly indicate that the silver, gold and copper nanoparticles might have a superior activity and rapid onset of action against the Gram negative bacteria E. coli and Salmonella spp. and the Gram positive bacteria Staphylococcus aureus with diarrheal origin.