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Purpose To investigate the frequency of hypogonadism and its relationship to inflammation and carotid intima-media thickness (CIMT) in male patients with predialysis chronic kidney disease (CKD). Methods A total of 105 patients with CKD, 55 (52.4%) as stage 3, 33 (31.4%) as stage 4 and 17 (16.2%) as stage 5, were enrolled into the study. Total testosterone (TT) and free testosterone (FT), interleukin 6 (IL-6), C-reactive protein (CRP) levels, and CIMT were measured. Results According to TT and FT, hypogonadism was detected in 18 (17.1%) and 22 (20.9%) patients, respectively. There was no difference in terms of TT and FT, CIMT, CRP and IL-6 between the stages of CKD. According to TT, the patients with hypogonadism had significantly higher CRP and high-density lipoprotein cholesterol (HDL-cholesterol) levels (p = 0.004 and p = 0.005, respectively). There was no significant difference in other parameters. According to FT, the patients with hypogonadism had significantly higher CRP (p = 0.017), and TT were negatively correlated with body mass index (BMI), waist circumference (WC), hip circumference, and CRP levels. FT was negatively correlated with age, waist circumference, systolic blood pressure, diastolic blood pressure (DBP) and CRP. Conclusions The frequency of hypogonadism was found around 17–21% among the patients with CKD. Despite similar IL-6 and CIMT levels, CRP was found to be higher in the patients with hypogonadism. We consider that further studies with larger populations are needed to elucidate the entity.