The objective of this case-control study was to determine the association between herbal medicine use during pregnancy and perinatal mortality in Tumpat District, Kelantan, Malaysia. Cases were mothers who gave birth from June 2002 to June 2005 with a history of perinatal mortality, while controls were those without a history of perinatal infant mortality. A total of 316 mothers (106 cases and 210 controls) were interviewed. The use of unidentified herbs prepared by traditional midwives and other types of herbal medicines during the first trimester of pregnancy were positively associated with perinatal mortality (OR = 5.24, 95% CI = 1.13; 24.23 and OR = 8.90, 95%, CI = 1.35; 58.53, respectively). The use of unidentified "Orang Asli" herbs and coconut oil during the third trimester of pregnancy were negatively associated with perinatal mortality in Tumpat (OR = 0.10, 95% CI = 0.02; 0.59 and OR = 0.48, 95% CI = 0.25; 0.92, respectively). These findings suggest the use of unidentified "Orang Asli" herbs and coconut oil in late pregnancy are protective against perinatal mortality, while the use of unidentified herbs prepared by traditional midwives and other types of herbal medicines in early pregnancy has an increased risk of perinatal infant mortality. Pharmacological studies to confirm and identify the compounds in these herbs and their effects on the fetus should be conducted in the future.