Objectives: To compare carriage rates of Staphylococcus aureus in patients with and without chronic kidney disease (CKD) and identify associated factors. Results: We enrolled 64 CKD (A-1 = 13, A-2 = 17, A-3 = 34) and 56 non-CKD controls (B). Patients were categorized as: stage 5 CKD on haemodialysis (A-1), stage 5 CKD not on haemodialysis (A-2), renal transplant recipients with glomerular filtration rate > 60 ml/min (A-3) and those having chronic medical diseases with glomerular filtration rate > 60 ml/min/m2 (B). Median age = 57 years (range = 17–77). Nasal or axillary Staphylococcus aureus carriage was seen in 5 (38.5%), 2 (11.8%), 5 (14.7%) and 9 (16.1%) patients from A-1 to A-3 and B groups respectively. All isolated organisms were methicillin sensitive. Haemodialysis (p = 0.035) and antibiotic use in the preceding month (p = 0.02) were associated with carriage. Demographic factors and co-morbidities were not associated with carriage.