Introduction: Glomerular hyperfiltration leads to hypertension, microalbuminuria, and impaired renal function in children with congenital solitary functioning kidney (cSFK). The purpose of this study was to investigate the associations between serum transforming growth factor beta-1 (TGF) and endoglin levels and hypertension, renal function or microalbuminuria in children with cSFK. Materials and Methods: 63 patients and 36 controls were included in the study. Serum endoglin and TGF-beta 1 level was measured using ELISA commercial kits. Results: Serum TGF-beta 1 and endoglin levels were higher in patients than those of controls (P = 0.04 and P < 0.001, respectively). The prevalence of hypertension was found to be 45.6%. There was a positive association between endoglin levels and the presence of masked hypertension (odds ratio: 1.121, P = 0.04). TGF-beta 1 and endoglin levels were positively associated with microalbuminuria (OR: 1.17, P = 0.04; OR: 1.836, P = 0.01). ROC curve analysis showed that serum endoglin and TGF-beta 1 levels had predictive value for microalbuminuria (cut-off value: 4.86 ng/mL, sensitivity: 94.7%, specificity: 54.5%, area under the curve +/- standard error [ AUC +/- SE]: 0.888 +/- 0.025, P = 0.01 for endoglin; cut-off value 561.24 pg/mL, sensitivity: 89.5%, specificity: 73%, AUC +/- SE: 0.995 +/- 0.334, P = 0.02 for TGF-beta 1). There were no significant relationships between glomerular filtration rate and serum TGF-beta 1 or endoglin levels. Conclusions: Endoglin and TGF-beta 1 may play an important role in the pathophysiology of microalbuminuria in cSFK. Endoglin may have a role in the development of hypertension in children with cSFK.