Despite increasing interest in minimally invasive surgery, prevalence data are completely absent. Our objective was to analyze clinico-epidemiological variations of surgery for renal malignancy in Japan with emphasis on annual trends and regional gaps, and to analyze factors affecting choice of open versus minimally invasive surgery. We identified patients who underwent open (n=8646), laparoscopic (n=5932), or minimum incision endoscopic surgery (MIES) (n=381) nephrectomy for renal malignancy, using the Japanese Diagnosis Procedure Combination database, 2007-2010. Clinical and regional variations in these three approaches were determined, and the annual per-population incidence of nephrectomy was estimated. Multivariate logistic regression was used to analyze factors affecting choice of minimally invasive surgery (laparoscopy or MIES). The proportion of open nephrectomy decreased from 65.3% in 2007 to 51.6% in 2010. Laparoscopic nephrectomy accounted for 51.0% of procedures for T1 tumors. The estimated incidence of nephrectomy in males and females was 14.3 and 6.1 per 100,000person-years, respectively. Multivariate analysis showed that minimally invasive nephrectomy was more likely to be selected for patients in their 30-50s who had less comorbidity, better performance status, or lower TNM stage, in high-volume or academic hospitals, especially in western Japan. Hemodialysis use was a favorable factor. Despite differences between eastern and western Japan, minimally invasive surgery is becoming widespread throughout Japan, especially for patients with low operative risks and early-stage cancer who are hospitalized in high-volume institutes.