Background Chronic kidney disease (CKD) is associated with aging, diabetes, hypertension, dyslipidemia, obesity, and unhealthy lifestyle behaviors and has become a public health burden worldwide. Methods We investigated the trends of CKD prevalence over a period of 16 years in Korean adults based on the Korean National Health and Nutrition Examination Survey (KNHANES): phase I (1998), II (2001), III (2005), IV (2007-09), V (2010-2012), and VI (2013). Of the 105,504 individuals aged over 20 years who participated in KNHANES I-VI, 55,191 (23,729 men and 31,462 women) were included in the present study. Results The sequential percentage of glomerular filtration rate (GFR)\60 ml/min/1.73 m(2) in KNHANES I-VI was 1.0, 4.2, 3.2, 1.9, 1.6, and 2.1 % in men and 3.6, 9.3, 10.4, 3.1, 1.6, and 2.0 % in women, respectively. The percentage of proteinuria >= 1 + in men rebounded after KNHANES V (3.1, 2.9, 2.8, 1.9, 1.1, and 1.7 % in KNHANES I-VI, respectively), but in women declined across all KNHANES reads (3.4, 2.3, 1.4, 1.6, 1.0, and 0.9 %, respectively). The prevalence of CKD rebounded after KNHANES V for men (3.9, 6.8, 5.5, 3.5, 2.4, and 3.5 % in KNHANES I-VI) while those in women decreased to a plateau level (6.6, 10.9, 11.4, 4.2, 2.4, and 2.4 % in KNHANES I-VI, respectively). Conclusions Our study shows that the prevalence of CKD in Korean adults has decreased overall, but since KNHANES V there has been a rebound in men while no changes in women.