<i>Background/Aims:</i> The commonly used kidney function tests have limitations, especially in thyroid dysfunction. Therefore, we studied the most commonly used kidney function tests in patients with hypo- and hyperthyroidism and after reaching euthyroidism. <i>Methods:</i> Prospective case series in 16 patients with thyroid dysfunction. Serum creatinine, 24-hour creatinine clearance, calculated glomerular filtration rate (GFR) by Cockroft-Gault, estimated GFR (eGFR) by the Chronic Kidney Disease Epidemiology Collaboration equation, serum cystatin C, eGFR based on cystatin C, eGFR based on a combined (cystatin C and creatinine) formula and plasma neutrophil gelatinase-associated lipocalin (NGAL) were measured in hypo- and hyperthyroidism and after gaining euthyroidism. <i>Results:</i> When free thyroxine (fT₄) normalized in hypothyroid patients, creatinine decreased and creatinine-based eGFR increased significantly. In contrast, cystatin C increased and eGFR based on cystatin C decreased significantly. There was no significant change in NGAL levels. When fT₄ normalized in patients with hyperthyroidism, creatinine increased and creatinine-based eGFR decreased significantly. In contrast, cystatin C decreased and cystatin-C-based GFR increased significantly. There was no significant change in NGAL levels. <i>Conclusions:</i> Thyroid function has a major influence on the vast majority of kidney function tests. Cystatin C is strongly influenced by the thyroid function and should be avoided in thyroid disorders. There was no effect on the plasma NGAL levels. The recommended kidney function test is a measurement of creatinine-based eGFR.