The aim of this study was to investigate the association between serum biomarkers and oral health parameters in children with chronic kidney disease (CKD). Serum hemoglobin, blood urea nitrogen, serum creatinine, calcium, parathormone, magnesium, and phosphorus levels were measured in 62 children with CKD aged between 4 and 17years. Intraoral examinations of the patients were performed by two different pediatric dentists. Dental caries was assessed using the decayed-missing-filled-teeth (DMFT/dmft) indexes, and oral hygiene was assessed using the debris (DI), calculus (CI), and simplified oral hygiene (OHI-S) indexes. Spearman's rho coefficient and generalized linear modeling were used to examine the association between serum biomarkers and oral health parameters. The results of the study showed that there were negative and statistically significant correlations between serum hemoglobin and creatinine levels and dmft scores in pediatric patients with CKD (p = 0.021 and p = 0.019, respectively). Furthermore, blood urea nitrogen levels and DI and OHI-S scores (p = 0.047 and p = 0.050, respectively); serum creatinine levels and DI, CI, and OHI-S scores (p = 0.005, p = 0.047, p = 0.043, respectively); and parathormone levels and CI and OHI-S scores (p = 0.001 and p = 0.017, respectively) were found to be positively and statistically significantly related. There are associations between various serum biomarker levels and dental caries and oral hygiene parameters in pediatric patients with CKD. The impact of changes in serum biomarkers on oral and dental health is important for dentists' and medical professionals' approaches to patients' oral and systemic health.