OBJECTIVE To compare the distance between the colon and the trajectory of percutaneous nephrolithotomy (PCNL) access both in prone and flank-free modified supine (FFMS) positions as measured on computed tomography and to study the effect of age, gender, BMI, side, and previous renal surgery as influencing factors. PATIENTS AND METHODS In this prospective study, we included 367 patients scheduled for PCNL. All patients underwent low dose abdominal computed tomography both in prone and FFMS positions. Patients <18 years and those with previous colonic surgery or renal congenital anomalies were excluded. The perpendicular distance between the imaginary line of the renal access and the colon was measured. Findings were correlated to different influencing factors. RESULTS Two hundred nineteen patients were males, and 148 were females. BMI of <30 were reported in 158 patients whereas BMI >30 in 209 patients. Data analysis showed that the mean perpendicular distance between colon and the renal access in FFMS and prone positions were 35.92 ± 0.22 mm and 17.78 ± 0.09 mm, respectively. In prone position only obesity, age, and overall interaction effect were the significant factors on the studied distance. In FFMS position, in addition to the effect of the prior factors, previous renal surgery also significantly reduces this distance. CONCLUSION The distance between the colon and assumed PCNL trajectory at a puncture on the posterior axillary line was influenced mainly by patient position. In FFMS position the colon appears to be farther than in prone position. BMI and age significantly influence this distance to a lesser extent.