Abstract: BACKGROUND: Prematurity is associated with lots of comorbidities. Premature neonates also have lower bone mineral content (BMC) compared to term neonates. Apnea of prematurity is a common complication and caffeine citrate is widely used for its prevention and treatment. Caffeine also affects creatinine clearance, urine flow rate and releases calcium from its storage sites. OBJECTIVES: The primary objective was to assess BMC in preterm neonates treated with caffeine using dual energy X-ray absorptiometry (DEXA). Secondary objectives were to determine whether caffeine therapy is associated with increased incidence of nephrocalcinosis or bone fracture. METHODS: Prospective observational study on 42 preterm neonates, 34 weeks’ gestation or less; 22 of them received intravenous caffeine (caffeine group) and 20 did not (control group). Serum levels of calcium, phosphorus, alkaline phosphatase, magnesium, sodium, potassium, and creatinine, abdominal ultrasonography, and DEXA scan were done for all included neonates. RESULTS: BMC showed significant lower levels in the caffeine compared to control group (p = 0.017). Additionally, BMC was significantly lower in neonates who received caffeine for more than 14 days compared to those who received it for 14 days or less(p = 0.04). BMC showed significant positive correlation to birth weight, gestational age, serum P and significant negative correlation to serum ALP. Caffeine therapy duration was negatively correlated to BMC (r = –0.370, p = 0.000) and positively correlated to serum ALP levels (r = 0.667, p = 0.001). None of the neonates had nephrocalcinosis. CONCLUSIONS: Caffeine administration for more than 14 days in preterm neonates may be associated with lower BMC but not nephrocalcinosis or bone fracture.