The characteristics of clinically insignificant residual fragments (CIRFs) are well described after percutaneous nephrolithonomy (PCNL) and shock wave lithotripsy (SWL). In follow-up procedures, CIRFs are associated with obstruction, infectious conditions, and recurrent stone development. In this study, we aim to determine the medium-term outcomes of CIRF. Between May 2009 and January 2013, 384 patients underwent flexible ureterorenoscopy (F-URS). In 44 patients, CIRFs were diagnosed with abdominal CT between 3 weeks and 3 months after the operation. Periodic follow-up, including clinical examination, serum biochemistry, urine culture, and radiological imaging, was performed for all patients. Also, 24 h urine analysis and stone composition were evaluated. Asymptomatic patients with stable stone sizes or patients with spontaneous clearance were classified in group 1 and patients with increasing stone sizes or those who became symptomatic were classified in group 2. The variables affecting stone recurrence between the two groups were compared. A total of 15 patients showed symptoms and/or stone development in the median 30.5 +/- A 8.809 months follow-up period. Additional treatment modalities-including F-URS in five patients, URS in three patients, SWL in two patients, and PCNL in one patient-were performed in 11 patients. The pre-operative stone burden and the number of patients with metabolic abnormalities were significantly higher in group 2 than in group 1. Medium-term follow-up of CIRF after F-URS demonstrated that recurrence is common within 2 years. The presence of a pre-operative high stone burden and metabolic abnormalities in 24 h urine analysis were predictive factors for stone recurrence.