BACKGROUND Endodontic emergency during root canal treatment (flare up) is a common occurrence in multivisit root canal treatment (RCT) and it may be associated with many factors. The occurrence however can affect the prognosis of the tooth and the patient -clinician relationship. OBJECTIVE To determine the incidence and risk factors associated with occurrence of flare up in a multi visit RCT. METHODS Patients planned for multi-visit (RCT) were recruited for the research. Standard protocol was followed in all cases. After the first visit, the patients were followed up for possible development of flare up. Patients' demographics, presence or absence of preoperative pain, status of the pulp and occurrence of flare up were among the data collected. Data was analyzed using SPSS version 20 with level of significance set at P <0.05. RESULTS A total of 106 root treated teeth were analyzed in patients aged 17 to 73years with a mean of 33±13.2 and male to female ratio of 1:1.5. Incidence of flare up was 8.5%. Prior to treatment, 47% of the cases had pain, 61.3% had apical radioluscency and 83% had pulpal necrosis. Majority (7, 77.8%) of the flare up occurred after the first visit (p=0.000). Only pre- treatment pain had a statistical significant ielationship with occurrence of flare up (p=0.009). CONCLUSIONS Incidence of flare up was 8.5% and the major risk factor was preoperative pain. First visit in a multi visit RCT is an important stage which if well handled, can reduce the incidence of flare up.