End-stage renal disease (ESRD) is a serious public health problem in Guangxi, a province of south China. This prospective study evaluated the characteristics and outcome of rural patients with ESRD in a dialysis center of Guangxi, compared with urban patients in the same period. A total of 238 patients (96 rural and 142 urban) who enrolled in 2007 was included in this study and followed up for 1 year. Clinical data including patient basic information, clinical parameters, laboratory tests, data associated with dialysis and prognosis were evaluated and compared between rural and urban groups. Glomerulonephritis was found to be the most common cause of ESRD in all the cohorts studied, with similar rates of 47.9 and 46.5% in the rural and urban patients, respectively. Compared to urban patients, the rural patients had significantly lower prevalence of diabetic nephropathy (8.3 vs. 24.6%, P < 0.001) and higher prevalence of obstructive uropathy (20.8 vs. 3.5%, P < 0.001); the rural patients were overall younger, with poorer financial supports, but with higher rates of late referrals, poorer renal functions as indicated by related laboratory tests including lower levels of GFR, serum hemoglobin, bicarbonate and Kt/V, but higher prevalence of very low GFR, severe metabolic acidosis, severe anemia and hyperkalemia, higher rate of not initiating dialysis, radial artery puncture and mortality. The cardiovascular events were found to be the most common cause of death in both rural and urban groups. Glomerulonephritis was found to be the most common cause of ESRD in all the studied patients. The rural patients with ESRD in Guangxi had kidney disease in more advanced stage at the time of first visit to a nephrologist and higher rates of mortality after dialysis initiation, compared to urban patients.