This study aimed to investigate whether continuous, low-dose, intracerebral infusion of either brain-derived neurotrophic factor (BDNF) or neurotrophin-3 (NT-3) could protect against striatal neuronal loss in mild neonatal hypoxic/ischaemic brain injury. Continuous, low-dose, intracerebral treatment is likely to minimise unwanted side effects of a single high dose and lengthen the time window for neuroprotection. A milder, albeit brain damage-inducing, hypoxic/ischaemic injury paradigm was used since this situation is likely to produce the highest survival rates and thus the greatest prevalence. Anaesthetised postnatal day 7 rats were each stereotaxically implanted with a brain infusion kit connected to a micro-osmotic pump. The pump continuously infused either BDNF (4.5 microg/day), NT-3 (12 microg/day), or vehicle solution into the right striatum for 3 days from postnatal day 7. The intrastriatal presence of BDNF or NT-3 was verified immunohistochemically. On postnatal day 8, the rats underwent right common carotid artery ligation followed by hypoxic exposure for 1.5 h. Animals were weighed daily thereafter and killed 1 week later on postnatal day 14. The total number of medium spiny neurons within the right striatum was stereologically determined using an optical disector/Cavalieri combination. Other measures of neuroprotection such as brain weight and striatal infarct volume were also undertaken. BDNF or NT-3 significantly increased the total number of surviving medium spiny neurons by 43% and 33% respectively. This significant neuroprotection was not evident when brain weight, striatal volume, striatal infarct volume, and neuronal density measures for NT-3, were compared. These measures therefore missed the protective effect demonstrated by the total neuronal count. This suggests that stereological measurement of total neuronal number is needed to detect neuroprotection at 1 week after low-dose, continuously infused, neurotrophin treatment and mild hypoxic/ischaemic injury. The results also suggest that lower treatment doses may be more useful than previously thought. BDNF may be particularly useful since it fostered both neuroprotection and normal weight gain. The ability to rescue striatal neurons from death may contribute toward a potential short-term, low-dose neurotrophin treatment for mild perinatal hypoxic/ischaemic brain injury in humans.