The objective of this study was to present the outcomes of comparative clinical study of microperc versus mini-percutaneous nephrolithotomy (mini-PNL) in the treatment of lower calyx stones of 10-20 mm. Patients with lower calyx stones treated with microperc (Group-1) or mini-PNL (Group-2) between 2011 and 2014 were retrospectively analyzed. Demographics of the patients were compared, including age, gender, BMI, stone size, laterality and procedural parameters (operation and fluoroscopy time), and outcomes (success and complication rates). A total of 98 patients were evaluated, assigned to Group-1 (n = 58) and to Group-2 (n = 40). Groups were statistically similar in terms of age, stone size, and BMI (p = 0.3, 0.07, 0.6, respectively). The mean procedure and fluoroscopy duration for Group-1 were 43.02 +/- A 27.98 min and 112.05 +/- A 72.5 s, and 52.25 +/- A 23.09 min and 138.53 +/- A 56.39 s in Group-2 (p = 0.006 and 0.006). The mean hematocrit drop was significantly higher in Group-2 compared to Group-1 (3.98 vs. 1.96 %; p < 0.001); however, none of the cases required blood transfusion. Overall complication rates exhibited no statistically significant difference (p = 0.57). Stone-free status was similar (86.2 vs. 82.5 %, p = 0.66). The tubeless procedure rate was significantly higher in Group-1 (p < 0.001). In Group-2, duration of hospitalization was significantly longer than in Group-1 (2.63 vs. 1.55 days; p < 0.01). Outcomes of the present retrospective study show that microperc is a treatment option for medium-sized lower calyx stone, being associated with lower blood loss, procedure, reduced fluoroscopy and hospitalization time, and a higher tubeless rate.