Diagnosis of perinatal infection in the newborn is difficult; there may be few clinical signs and current tests are slow or non-specific. Detection of organisms, antigen or specific antibody to common pathogens often requires repeat samples and does not give immediate results. Haematological parameters, although relied upon frequently to diagnose infection in the neonate prior to a positive bacterial isolation, are unreliable and insensitive. Indicators such as an increase in neutrophil band cell counts are highly variable between morphologists. Infection induces the expression of a number of T lymphocyte surface markers, including CD45RA/CD45RO and CD45RO. The use of changed expression of surface markers as a laboratory test for detection of infection in neonates was evaluated. We used multiparameter flow cytometry to detect expression of early (CD45RA/CD45RO) and late (CD45RO) activation markers. In the respective groups of 50 full term (including 25 normal vaginal deliveries and 25 caesarean deliveries) and 30 premature, i.e. < 36 weeks gestation (born by either normal vaginal delivery or caesarean delivery) the CD45RA isoform was brightly expressed on newborn 'naive' CD4+ T cells, whereas the CD45RO isoform (including both 'bright' and 'dim' populations) was present on < 19% of CD4+ T cells from these newborn infants. In a group of 37 infants, tested to evaluate possible effects of non-infective parameters such as respiratory distress and iso-immunization, no significant changes in surface marker expression were found and specificity of the test was confirmed. In 14 neonates with documented sepsis, up-regulation of dual staining CD45RA/CD45RO isoforms on CD4+ T cells was detected early in the infection. In addition, we found that CD45RO expression persisted for several weeks after bacterial infection, and up to several months in viral infection. In conclusion, detection of T cell activation by flow cytometry for the early diagnosis of neonatal infection is an easy test to carry out on small volumes of blood, is inexpensive, and may be a specific indicator of infection.