Background: Timely breastfeeding initiation (BFI) decreases the risk of neonatal mortality and ensures breastfeeding continuation. Mothers need the assistance of trained staff to initiate breastfeeding timely. This study examined the factors associated with delayed BFI among mothers attending breastfeeding support clinics. Methods: a cross-sectional study was conducted on 200 mothers from three randomly chosen family health units in Alexandria. Mothers were interviewed to answer questions about demographic data, health service-related data (mode of delivery, neonatal illness, help offered by staff for BFI and the practice of “rooming-in" and questions about breastfeeding practices and barriers they faced for BFI. Results: Mothers with successful BFI represented 55 % of the sample. Cesarean delivery was associated with delayed BFI compared to vaginal delivery (55.7% vs 15.1% p < 0.001). A higher percentage of infants with medical conditions and infants admitted to the Neonatal Intensive Care Unit (NICU) were associated with delayed BFI (57%,71.6% respectively). In addition, receiving of prenatal advice, hospital staff assistance and “rooming-in" were all associated with timely BFI (p=0.021, <0.001, <0.001, respectively). Cesarean delivery has been proven a significant risk factor for delayed BFI (OR=11.692, 95% CI=3.922-34.86, p < 0.001). Furthermore, NICU admission and lack of health staff assistance for BFI were significant risk factors for delayed BFI (OR=4.633, 95 % CI=1.835-11.698, p=0.001 and OR= 3.175, 95% CI=1.084 - 9.297, p=0.035 respectively). Conclusions: Delayed BFI is common. High risk groups such as cesarean delivery and NICU admission need more BFI support and monitoring. Health facilities need training to implement the Baby-friendly Hospital Initiative.