Simple renal cyst has controversy related to hypertension and renal dysfunction. We analyzed the impacts of cyst on hypertension and renal dysfunction, focusing on elimination of the confounding factors. We grouped 436 patients and 436 controls by characteristics of cyst and stratified with clinical parameters among 6603 patients who had routine health check-up in Seoul National University Bundang Hospital, Seongnam, Korea. The presence of cyst was related to hypertension but not to renal dysfunction. The number and the size of cyst were independent risk factors to the prevalence of hypertension. The presence of multiple renal cysts was related to hypertension in males, in persons over the age of 60 years, in persons with glomerular filtration rate (GFR) more than 60 ml/min/1.73 m2, or in persons without proteinuria. The effect of the large cyst and the peripheral cyst on the prevalence of hypertension was similar to that of the multiple cyst. The blood pressure of the multiple-cyst group, the large-cyst group, or the peripheral-cyst group was higher than that of the single-cyst group, the small-cyst group, or the perihilar-cyst group, respectively, regardless of antihypertensive medications. In conclusion, the presence of cysts or characteristics of cyst were not related to the decreased GFR. In conclusion, the presence of simple renal cyst was related to hypertension but not to renal dysfunction. The effect of simple cyst on hypertension was evident in males, aged persons, and persons without the evidence of renal disease. The number, size, and location were important characteristics of cyst related to hypertension.