Minimal invasive percutaneous nephrolithotomy (MPCNL) has been commonly used in removing urinary stones. However, the detrimental effects of clinically insignificant residual fragments (CIRF) after MPCNL have not been entirely clarified. This study is aimed at investigating the clinical outcomes of CIRF after MPCNL. From July 2004 to June 2010, 1862 cases of urolithiasis underwent MPCNL. 185 cases of CIRF were subsequently diagnosed using CT scanning and followed up. During follow-ups, medical history, physical examination, routine blood and urine tests, subjective symptoms were recorded. A multiple-variable Cox regression was performed to evaluate the prognostic significance of different factors for CIRF after MPCNL. Of 185 cases of CIRF followed up for 31.4 months on average, 58 cases (31.4%) suffered symptomatic episodes, including 30 cases of hematuresis, 21 cases of low urinary tract symptoms and 7 cases of hematuresis complicated with renal colic. The results of Cox regression showed that past history of extracorporeal shock wave lithotripsy (ESWL), CIRF size, hypercalcuria and CIRF located in ureteropelvic junction (UPJ) are independent risk factors for medium-term symptomatic episodes of CIRF after MPCNL. We suggest that regular follow-ups should be considered for patients with CIRFs after MPCNL for timely treatments, especially for those who are hypercalcuria-complicated, have history of ESWL, or suffer relatively large CIRFs located in the UPJ.