Mainzer-Saldino syndrome (MSS) or conorenal syndrome (CRS) is a rare autosomal recessive ciliopathy characterized by multiorgan affection, typically presents with a triad of nephronophthisis (NPHP), retinitis pigmentosa (RP), and cone-shaped epiphysis (CSE) with varying degrees of severity. A 20-month-old male is experiencing recurrent pneumonia attacks, an elevated serum creatinine level, proteinuria, and high anion gap partially compensated metabolic acidosis were incidentally discovered during one of his hospitalizations. A biopsy was performed, and the results supported the diagnosis of Alport syndrome. However, a subsequent genetic test suggests the presence of MSS. Aside from NPHP, RP and CSE tested positive. Based on the fact that MSS is not a common cause of end-stage renal disease (ESRD) in pediatrics, physicians should bear in mind genetic testing as a decisive tool. In this context, we highlighted a case of an accidentally discovered impaired renal function from first presentation to final diagnosis, with a valuable comparison with previously published similar cases.