Over the years, various anti-malarial drugs have been introduced to combat malaria parasite, with coartem and chloroquine being widely prescribed in hospitals in Nigeria. This study was designed to investigate the effect of coartem and chloroquine separately administered, on serum lipid profile which gives important preliminary information on possible adverse effect on cardiovascular health. Thirty male Wistar rats weighing 180 – 200 g were used for this study. After 7 days of acclimatization, the animals were divided into 2 batches (n = 15); thus A (3 days treatment) and B (7 days treatment). Each batch was further divided into 3 groups (n = 5) as follows; control, coartem treated group and chloroquine treated group. The treatment lasted for 3 days and 7 days for batch A and B respectively. The drugs were orally administered and all animals had access to food and water ad libitum. Blood was collected via cardiac puncture for lipid profile analysis. Results showed that serum total cholesterol was significantly (P<0.05) higher in the 7 days coartem treated group, compared with the 3 days coartem treated group. Low density lipoprotein and atherogenic index were significantly (P<0.05) increased in the 7 days coartem treated and chloroquine treated group, compared with the 3 days coartem treated and chloroquine treated group respectively. We therefore conclude that administration of either coartem or chloroquine for 3 days is safe, but can predispose to cardiovascular diseases secondary to altered serum lipid profile if administered for 7 days.