Background & Objectives: Oral anti-malarial therapy has been associated with varied gastrointestinal disorders with limited information on the effects on intestinal microflora. This study investigated the effects of chloroquine, Amodiaquine and Artesunate-Amodiaquine therapies on human intestinal lactic acid bacteria flora along with the anti-malaria efficacies and bowel functions. Methodology: Venous blood samples were collected from 30 human subjects of both males and females, aged between 20 and 30 years. Malaria parasitemia was determined along with faecal lactic acid bacteria (LAB) population prior to and after 3 days of oral administration of anti-malaria drugs. Results: The three anti-malaria drugs showed significant (P<0.05%) malaria parasite clearance with Artesunate-Amodiaquine being the most effectives at 67.3%, whereas chloroquine (32.9%) was the least. However, chloroquine showed highest stimulation of the intestinal LAB population (23.6%), whereas Artesunate-Amodiaquine significantly (p<0.05) reduced the mean LAB numbers by 87.3%. The Chi-Square (X2) analysis showed significant (p<0.05) association between the increase in faecal volume and LAB population among subjects administered the drugs. Conclusion: The anti-plasmodia efficacies of chloroquine and amodiaquine with mild effects on intestinal probiotic population indicate the beneficial use as anti-malaria prophylaxis, whereas artesunate-amodiaquine with high anti-malaria and anti-probiotic activities would be best for treatment of acute malaria.