The objective of this study was to determine the incidence and risk factors of nephrocalcinosis (NC) in pre-term neonates in the neonatal intensive care unit (NICU) at the Al-Minya University, Egypt. The study included 97 pre-term neonates with a gestational age 34 weeks. Data on duration of hospitalization, sex, gestation, birth weight, family history of renal stone, need for respiratory support, intake of calcium and use of total parenteral nutrition (TPN) and nephrotoxic drugs were collected. Blood urea nitrogen, serum creatinine, sodium, potassium, calcium and phosphate were measured within the first week of life and again at term. Blood gases, urinary pH, urinary calcium/creatinine (U Ca/Cr) ratio and urinary oxalate/creatinine (U Ox/Cr) ratio were measured once at term. Three renal ultrasound (US) scans were performed; one before the first week of life, the second at term and the third at a corrected age of one year. Of the 97 infants studied, 14 (14.4%) developed NC diagnosed by renal US at term. NC was bilateral in 11 infants. Factors significantly associated with NC were gestational age, need for respiratory support, high calcium intake, TPN, use of post-natal dexamethasone, furosemide, theophylline, and/or aminoglycosides and U Ca/Cr ratio and U Ox/Cr ratio (all P < 0.05). Low gestational age (P = 0.004), use of respiratory support (P = 0.005), furosemide therapy (P = 0.002) and increased U Ca/Cr ratio (P = 0.001) were the strongest independent risk factors after logistic regression analysis. Eight of the 14 infants (57.1%) with NC had spontaneous resolution of calcification at a corrected age of one year. Screening at term with a renal US scan and long-term follow-up of renal function is needed for early diagnosis and better management of NC. Future research pertaining to prevention of NC in pre-term neonates is required.