Abstract Background Research has indicated that the environment may play an important role in the transmission of meticillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile in healthcare facilities. Despite the significance of this finding, few data exist from longitudinal studies investigating MRSA and C. difficile contamination, concurrently, in both patient rooms and the general ward environment. The objectives of this study were to determine the prevalence of MRSA and C. difficile contamination in patient rooms and the ward environment and identify risk factors associated with a surface being contaminated with these pathogens. Methods Environmental surfaces in patient rooms and the general environment in the medical and surgical wards of a community hospital were sampled six times over a 15 week period. Sterile electrostatic cloths were used for sampling and information pertaining to the surface sampled was recorded. MRSA isolates and C. difficile specimens were obtained from hospitalized patients. Enrichment culture was performed and spa typing or ribotyping was conducted for MRSA or C. difficile , respectively. Exact logistic regression models were constructed to examine risk factors associated with MRSA and C. difficile contamination. Results Sixteen (41%) patient rooms had ≥ 1 surfaces contaminated with MRSA and/or C. difficile . For 218 surfaces investigated, 3.2% and 6.4% were contaminated with MRSA or C. difficile , respectively. Regression models indicated that surfaces in rooms exposed to a C. difficile patient had significantly increased odds of being contaminated with C. difficile , compared to surfaces in unexposed patient rooms. Additionally, compared to plastic surfaces, cork surfaces had significantly increased odds of being contaminated with C. difficile . For 236 samples collected from the ward environment, MRSA and C. difficile were recovered from 2.5% and 5.9% of samples, respectively. Overall, the majority of MRSA and C. difficile strains were molecularly identified as spa type 2/t002 (84.6%, n = 11) and ribotype 078 (50%, n = 14), respectively. Conclusions In patient rooms and the ward environment, specific materials and locations were identified as being contaminated with MRSA or C. difficile . These sites should be cleaned and disinfected with increased vigilance to help limit the transmission and dissemination of MRSA and C. difficile within the hospital.