There is growing interest in the use of probiotics in neonates. In particular, Lactobacillus rhamnosus, L. acidophilus, Bifidobacterium breve and B. longum have been well studied. Caesarean-section (CS)-born infants often lack Lactobacillus spp. and Bifidobacterium spp., which showed increasing evidence in establishing the neonatal immune system. Furthermore, CS increases the difficulties for mothers in initiating and sustaining breastfeeding. Increasing evidence shows CS-born infants are more susceptible to allergy, infections and chronic inflammatory diseases later in life. The number of CS births has increased continuously, now accounting for 35% of all deliveries Australia wide. In this context, probiotics may have a role in establishing a healthy neonatal gut microbiome.