Background: Antibiotic resistance of pathogenic bacteria is well recognized among clinicians; however, studies that directly evaluate the bacterial resistance to commonly used disinfectants in clinical settings are lacking. Currently available reports focus on the resistance of single strains to single disinfectants and do not adequately examine the degree of resistance and cross-resistance to antimicrobials in the large-scale clinical use of disinfectants. Methods: We investigated the resistance capacity to 11 antibiotics and 7 chemical disinfectants by bacterial strains collected from body fluids of patients in 10 hospitals in Beijing, China over a 1-year period. Bacterial resistance to disinfectants was tested using minimum inhibitory concentration and minimum bactericidal concentration using agar dilution methods based on commercially available reference strains. Results: A total of 1,104 pathogenic strains were identified, of which 23% were Gram-positive bacteria, 74% were Gram-negative bacteria, and 3% were fungi. Overall, resistance to antibiotics for the most common strains was significantly higher than their resistance to disinfectants. The least effective antibiotics and disinfectants were aztreonam and glutaral, respectively, exhibiting the highest overall resistance rates; while amikacin and alcohol had the lowest resistance rates. Consistently, Acinetobacter baumannii exhibited the most resistance, while Escherichia coli had the least resistance for both antibiotics and disinfectants. Conclusions: Based on the pathogen spectrum for bacterial infective pathogens evaluated in this study, as well as the status quo of their resistance to antimicrobial agents and common clinical disinfectants, it is essential for healthcare professionals to pay attention not only to the standardized use of antimicrobial agents but also to the rational application of disinfectants.