Abstract Background Much of the data on still births and early neonatal deaths from resource-limited settings are obtained via maternal recall from national or community level surveys. While this approach results in useful information to be obtained, often such data suffer from significant recall bias and misclassification. In order to determine the prevalence of stillbirths (SB), early hospital neonatal death (EHND) and associated factors in Blantyre, Malawi, a prospective study of pregnant and post-natal women was conducted at the Queen Elizabeth Central Hospital (QECH), Malawi. Methods A prospective observational study was conducted between February 1, 2004 and October 30, 2005. Consecutive women attending the hospital for delivery were recruited. Data were collected on the health status of the fetus on admission to labor ward and immediately after delivery, whether alive or dead. Gestational age (GA) and birth weight (BW) and sex of the newborn were also noted. Similar data were also collected on the live births that died in the delivery room or nursery. Data were analyzed using SPSS (Statistical Package for the Social Sciences) statistical package. Results A total of 10,700 deliveries were conducted during the 12 months study period and of these deliveries, 845 (7.9%) were SB and EHND. Stillbirths comprised 3.4% of all deliveries; 20.2% of the ante-partum deaths occurred before the mother was admitted to the labor ward while a slightly higher proportion (22.7%) of fetal loss occurred during the process of labor and delivery. Fifty-sex percent of the perinatal deaths (PD) were EHND. The mean gestational age for the perinatal deaths was 34.7 weeks and mean birth weight was 2,155 g (standard deviation = 938 g). The majority, 468 (57.8%) of the perinatal deaths were males and 350 (43.2%) were females. Many of the perinatal deaths (57.9%) were deliveries between gestational ages of 20 and 37 weeks. Most (62.7%) of the mothers with a perinatal death had experienced a previous similar incident. Conclusion About 3.4% of all pregnant mothers past 20 weeks of gestation ended up in delivering a stillbirth; another 4.4% of the live births died before discharge from hospital, thus, 7.9% of pregnancy loss after 20 weeks (or 500 g estimated weight) of gestation. This is a higher loss when compared to international and regional data. We recommend attention be given to these unfavorable outcomes and preventive measures or intervention for preventable causes be considered seriously. These measures could include the provision of emergency obstetric care, improving access to deliveries by health professionals and resourcing of health facilities such that neonatal viability is promoted.