Introduction Loss of barrier function of the intestinal wall resulting in translocation of bacteria and bacterial toxins is regularly cited in the pathogenesis of necrotising enterocolitis (NEC) but objective evidence before the onset of NEC is limited.

Objective To make serial measurements of bacterial DNA and LPS endotoxin in a population of preterm babies and compare those who developed NEC with those who did not.

Methods 16SrRNA Real-time PCR and ELISA were used to detect the presence of bacterial DNA and LPS endotoxin in blood and plasma from infants <31 weeks gestation sampled weekly for 4 weeks from 14 days.

Results Eighty six infants were enrolled [median (range) gestation 26.5 (23–30) weeks and median (range) birth-weight 859 (572–1800) g]; 23 infants (26%) developed NEC (any NEC) of whom 13 (15%) had ≥Bells Stage II NEC.

Bacterial DNA was detected in 5 infants, 3 of whom subsequently developed NEC. Babies with bacterial DNA were more likely to have ≥Bells Stage II NEC (p = 0.03) but not to have any NEC.

Fourteen babies were positive for LPS, 7 of whom developed NEC. LPS endotoxinaemia was associated with development of any NEC (p = 0.04) but not with ≥Bells StageII NEC.

Only 2 babies were positive for both16S rRNA and LPS all of whom developed ≥Bells Stage II NEC.

Conclusion Circulating bacterial DNA and endotoxin, probably entering the blood stream via the intestinal wall, were detected in a cohort of preterm babies and associated with the subsequent development of NEC.