Introduction: Medications produce a therapeutic effect that modulates a disorder and unwarranted effects that may be intrinsically harmful. Adverse drug reactions (ADRs) are undesirable effects that results from drug administration at usual doses and are the primary focus of regulatory agencies and post-marketing surveillance. Aim and objectives: To evaluate ADRs to Artemisinin-based Combination Therapies (ACTs) such as Artemether-Lumefantrine (AL) and Artesunate-Amodiaquine (AA) among adults with the objectives of (i) estimating and comparing the frequency of ADRs associated with AL and AA and (ii) developing a list of classical adverse drug reactions to both antimalarials. Materials and Methods: This cross-sectional, quantitative study was conducted from March to May 2013 at Ikorodu, a peri-urban settlement in Lagos State of Nigeria among 252 patients diagnosed with malaria and randomized into Artemether Lumefantrine (AL) arm and Artesunate Amodiaquine (AA) arm. Results: The mean age (years) of all the study subjects was 34.4 (10.6) with 58% of them who attained secondary level education. About 50% of them took other non-antimalarial medication together with prescribed ACT during their illness. Overall mean duration of illness (days) before taking ACT was 2.8 (1.14) which was significantly longer (t-est=-3.57, P-value=0.0002) in AA arm (3.1 ± 1.2) than in AL arm (2.6 ± 1.0). In all, 234 (96.4%) and 169 (67.1%) severally completed the full dose of treatment and ate pre-medication fatty meal. Overall prevalence of ADRs was 47.6% - 27.8% in the AL arm and 69.8% in the AA arm. Among those who did not take fatty meal, the risk of ADRs was higher (χ²=0.69, P-value=0.40, RR=1.26, 95% CI=0.72, 2.21) in the AA arm compared to the AL arm. Weakness, dizziness and headache were the most prevalent ADRs reported in both AL (25.9%, 13.8%, 15.5% respectively) and AA (50.0%, 10.0%, 16.4% respectively) arms. Conclusion: In general, the frequency of ADRs, though mild or moderate in severity, was significantly higher in the AA arm than in the AL arm and the frequency of serious ADR was very low. The most prevalent ADRs reported were weakness/fatigue, headache and dizziness. Pre-medication consumption of fatty meal reduced the frequency of ADRs in both arms of the study. Programmes on the management of malaria with ACT should consider this baseline information for active surveillance for ADRs in Nigeria.