Background: The risk factors for methicillin-resistant Staphylococcus aureus (MRSA) colonization can differ between acute-care, subacute-care, and long-term care facilities, but comparative information is lacking. We compared risk factors for MRSA colonization contemporaneously between an acute-care hospital (ACH) and its affiliated intermediate- and long-term care facilities (ILTCFs). Methods: Serial cross-sectional studies were conducted in a 1,600-bed tertiary-care ACH and its 6 affiliated ILTCFs in Singapore, in June–July 2014–2016. Separate nasal, axillary, and groin swabs were taken and cultured for MRSA. MRSA isolates were subject to whole-genome sequencing. Clinical and epidemiological data were obtained from medical records. To account for clustering, multivariable 2-level multinomial logistic regression models were constructed to assess factors associated with colonization of specific MRSA clones, in the ACH and ILTCFs, respectively. Results: In total, 8,873 samples from 2,985 patients in the ACH and 7,172 samples from 2,409 patients and residents in ILTCFs were included in the study. Patients and residents in the ILTCFs (29.7%) were more likely to be colonized with MRSA than patients in the ACH (12.6%) (P < .0001). The predominant MRSA clones were clonal complexes (CC)22 (n = 692, 46.7%) and CC45 (n = 494, 33.4%), contributing to 80% of MRSA isolates. For ACH patients, after adjusting for age, gender, comorbidities, prior exposures to antibiotics and percutaneous devices, presence of wounds, and screening year, prior MRSA carriage in the preceding 12 months was the strongest predictor of colonization with all MRSA clones: CC22 (aOR, 14.71; 95% CI, 6.17–34.48); CC45 (aOR, 7.75; 95% CI, 2.70–22.22); and others (aOR, 22.22; 95% CI, 3.83–125.00). Hospital stay >14 days was also positively associated with colonization with MRSA CC22 (aOR, 2.67; 95% CI, 1.22–5.88), but not the other clones. For ILTCF patients and residents, after adjusting for age, comorbidities, prior exposure to antibiotics, presence of wounds, and screening year, prior MRSA carriage was a significant predictor of colonization with MRSA CC22 (aOR, 2.72; 95% CI, 1.35–5.46), and CC45 (aOR, 2.36; 95 % CI, 1.06–5.24), but not with other clones. Additionally, prior exposure to a percutaneous device and being male were respectively positively associated with colonization by MRSA CC22 (aOR, 2.70; 95% CI, 1.19–6.17) and CC45 (aOR, 2.17; 95% CI, 1.11–4.26). Conclusions: Prior MRSA carriage was a common risk factor for colonization with the predominant MRSA clones in both the ACH and ILTCFs. Hospital stay >14 days and exposure to percutaneous devices were additional risk factors for CC22 colonization in the ACH and ILTCFs, respectively. Pre-emptive contact precautions for prior MRSA-carriers on admission and active screening for long-stayers in the ACH could prevent intra- and interinstitutional MRSA transmission.