INTRODUCTION Septic arthritis (SA) is a devastating infection with a high rate of sequelae. The aim of this retrospective study was to determine the epidemiology, clinically significant sequelae and risk factors for developing these sequelae in children admitted to our hospital with SA. METHODS Patients with bacteriologically and/or radiologically confirmed SA from January 1999 to December 2014 were identified from discharge and laboratory records. Data was collected through a retrospective review of the case notes. RESULTS A total of 75 patients (62.7% male) met the inclusion criteria. The median age at presentation was six years (range two weeks to 15 years), and six patients were neonates. Microbiologic aetiology was determined in 40 (53.3%) patients, with Staphylococcus aureus being the most common organism. 68.0% of the patients underwent arthrotomy, and the average hospital stay was 15.3 days. Sequelae of SA were observed in nine patients on follow-up. Univariate and multivariate statistical analyses showed that young age, pyogenic bacterial isolation and concomitant osteomyelitis were significant risk factors for developing sequelae. CONCLUSION Our study demonstrated that young age, pyogenic bacterial isolation and concomitant osteomyelitis are associated with a high risk of sequelae. Timely microbiologic diagnosis by novel polymerase chain reaction methods and the use of magnetic resonance imaging in high-risk children to identify adjacent infection could possibly prevent lifelong disabling sequelae in SA.