Background The BFHI program and timely breastfeeding initiation may be threatened by the worldwide rise in cesarean section deliveries, and this might promote prelacteal feeding. What is the current burden and determinants of delayed breastfeeding initiation among mothers, who gave birth via cesarean section? Subject and methods This was the baseline data of a prospective cohort study, where 529 healthy, singleton mother-newborn pairs were recruited consecutively at birth, from Gitwe district hospital in Rwanda. Results Overall, the burden of cesarean section delivery, delayed initiation of breastfeeding and prelacteal feeding were 38.8%, 17.0% and 6.0%, respectively. Rate of delayed breastfeeding initiation among mothers, who delivered by cesarean section was 37.6%, compared to 4.0% among those that delivered vaginally, p<0.001. Prelacteal feeds were given to 12.7% of the babies that were delivered by cesarean section, compared to 1.9% among those delivered vaginally, p<0.001. Use of probably unsafe water sources located in the household yards was strongly linked to both cesarean section delivery (p<0.000; OR=5.71; 95%CI=2.43, 13.41) and delayed breastfeeding initiation (p<0.000; OR=44.40; 95% CI 7.97, 247.32). Mothers delivered by c-section, who were prenatally exposed to potentially harmful substances, were more likely to delay breastfeeding initiation compared to unexposed mothers (p=0.001; OR=3.14; 95% CI 1.56, 6.31). Cesarean section delivery was more likely with HIV positive mothers (p=0.010; OR=7.14; 95% CI:1.61, 33.33), teenage and entrepreneur mothers. Rate of cesarean section delivery amongst HIV positive mothers was 88.9%, compared to 36.1% among HIV negative mothers. Conclusion and Recommendations HIV positivity and non-medical causes still drive the over-use of cesarean section for delivery in this rural community, and this impacted negatively on breastfeeding initiation, thereby promoting prelacteal feeding. The uncertain safety of the water sources and prenatal exposures to harmful social habits also need to be addressed. KEY WORDS: Breastfeeding initiation, cesarean section delivery, prelacteal feeds, unsafe water, antenatal breastmilk expression.