Background: Medical foods could be vehicles of pathogenic microbes for vulnerable people in the hospitals. Hospital kitchen is considered as the main source of this cross-contamination. Objectives: The current study aimed at investigating the frequency of bacterial species and their antimicrobial resistance patterns in foods, food handlers, and utensils compared with those of the clinical isolates in a hospital kitchen in Tehran, Iran. Methods: This cross sectional study was performed in a hospital in Tehran, Iran from April 2011 to January 2013. Accordingly, simple random sampling of raw and cooked food materials, swab samples of cooking utensils, and hands and noses of food staff were done. Clinical samples were collected from blood, urine, wound, and respiratory aspirates of patients with hospital acquired infections. Bacterial isolates were identified according to biochemical standard identification schema. Antimicrobial susceptibility of the strains was determined by disk diffusion method according to the CLSI (the clinical and laboratory standards institute) guidelines. Molecular diversity of indicator bacterial isolates of Staphylococcus aureus and Escherichia coli in the kitchen and those of the isolated ones from intensive care unit were also investigated by molecular typing method. The occurrence of cross-contamination was hypothesized based on the results of phylogenetic investigation and resistance biotyping. Results: Out of the 200 kitchen samples, S. aureus, E. coli, Acinetobacter spp., Pseudomonas spp., and Enterococcus spp. were isolated in frequencies of 15.5%, 8%, 2.5%, 0.5%, and 0.5%, respectively. Prevalence of multidrug resistant-methicillin resistant strains of S. aureus (MDR-MRSA) in the samples of the hospital kitchen vs the intensive care unit (ICU) was 18.7% (6/32), compared with 91.6% (22/24), respectively. Among the kitchen E. coli isolates, MDR pattern was detected in a frequency of 52.9%; the highest frequency was detected among the isolates of utensils. Although the results of the phylogenetic and resistance biotyping analyses did not confirm significant relationship between the isolates of the ICU and hospital kitchen, this similarity was confirmed among the strains isolated from the foods, food handlers, and utensils. In this regard, food staff and utensils were considered as the main sources of cross-contamination for S. aureus and E. coli, respectively. Conclusions: Weak health conditions of food workers and inadequate cooking to eliminate the contaminants during food processing were postulated as the main risk factors for transmission of these bacteria, through medical foods. into hospital.