An increase in percutaneous nephrolithotomy (PCNL) has been accompanied by an increase in complications. We identified the parameters affecting the severity of complications using the modified Clavien classification (MCC). From 2008 to 2013, 330 patients underwent complete supine PCNL using subcostal access, one-shot dilation, rigid nephroscopy, and pneumatic lithotripsy. We assessed the impact of the following factors on complication severity based on the MCC: age, gender, body mass index, hypertension, diabetes, previous stone surgery and extracorporeal shock wave lithotripsy, preoperative hemoglobin, renal dysfunction (creatinine >1.4 mg/dL), preoperative urinary tract infection, anatomic upper urinary tract abnormality (AUUTA), significant (moderate-severe) hydronephrosis, stone-related parameters (opacity, number, burden, location, staghorn, complex stones), anesthesia type, kidney side, imaging and calyx for access, tract number, tubeless approach, operative time, postoperative hemoglobin, and hemoglobin drop and stone-free results. The complication rate was 19.7% (MCC: 0=80.3%, I=6.4%, II=11.2%, ≥III=2.1%). On univariate analyses, only the following factors affected MCC: gender, preoperative hemoglobin, AUUTA, significant hydronephrosis, imaging for access, calyx for access, tract number, postoperative hemoglobin, hemoglobin drop and stone-free result. Renal dysfunction was accompanied by higher complications, yet the results were not statistically significant. Multivariate logistic regression analysis demonstrated renal dysfunction, absence of significant hydronephrosis, AUUTA, multiple tracts, lower postoperative hemoglobin, and higher postoperative hemoglobin drop as the significant parameters which affected MCC and predicted higher grades. The paper's limitations include a low number of cases in the higher Clavien grades and some subgroups of variables, and not applying some techniques due to surgeon preference. Many of the complete supine PCNL complications were in the lower Clavien grades and major complications were uncommon. Renal dysfunction, AUUTA, significant hydronephrosis, tract number, postoperative hemoglobin, and hemoglobin drop were the only factors affecting MCC.