AL combination was officially introduced for the treatment of uncomplicated malaria in Benin in 2004. At that particular time, the drug was not generally accessible to the population, but it is nowadays distributed to all public health facilities largely through collaborative efforts involving Benin’s NMCP and its technical and financial partners. The study described here was conducted, according to WHO protocol, in children aged 6–59 months, the group most vulnerable to malaria in countries such as Benin where malaria transmission is characterized as stable. Before the age of 5 years children have not developed effective anti-malarial immunity. Importantly, the follow-up period of 42 days, rather than the 28 days frequently used in studies of this type, allows assessment of the impact of new infections arising in each child. In this study an ACPR, without PCR correction, was observed in 75.6 % of the overall population with no significant difference between the two geographically separated study sites (78.3 % Djougou, 73 % Cobly; P = 0.56). This ACPR rate is higher than the 33.3 % obtained by Tinto et al. [
23] after 42 days of follow-up in children under 5 years treated with AL, likely the result of a very high rate of re-infection. No cases of ETF were observed in the study presented here. Moreover, the cases of LCF and LPF observed were all found to be the result of re-infections, giving an ACPR of 100 % after PCR correction. This result thus confirms that the efficacy of the AL combination for first-line treatment of uncomplicated falciparum malaria in Beninese children under 5 years of age remains acceptably high after more than 10 years’ use. However, it is important to consider whether using only the markers
msp1 and
msp2 might have contributed to this very low recrudescence rate. It is true that the markers recommended by WHO are
msp1,
msp2 and
glurp [
24], but these markers should be genotyped sequentially, from the higher to the lowest discriminatory power. Once the analysis of one marker has shown a new infection, the analysis should be stopped. If no evidence of new infection is detected with the first markers, the second marker should be analysed. If no new infection is detected, then the third marker should be used. This would mean that the result could be given with the genotyping of a single marker and the low rate of recrudescence in this study cannot be attributed to the use of only two markers. Furthermore, several studies [
25,
26] in which three markers were used also found very low recrudescence rates. Findings in this study are consistent with other therapeutic efficacy studies with AL conducted both in the past in Benin [
27,
28] and elsewhere in sub-Saharan African countries (SSA) in which the PCR corrected ACPR ranged from 96 to 100 % [
25,
26,
29,
30]. Participants with re-infections in the present study received quinine as a second-line treatment because routine health services in Benin lack the means to distinguish between recrudescences and new infections. However, it remains unclear whether quinine or the same ACT (AL) would be the optimal treatment in such cases. Given that nearly all recurrent parasitaemias were caused by new infections, it is reasonable to imagine that re-treating the child with the same ACT regimen, rather than with quinine, would be appropriate. However, other studies using treatment with AL after 28 or 42 days follow-up noted further recrudescences suggesting drug failure with, respectively, 82.4, 92 and 93 % of ACPR after PCR correction [
31‐
33]. Such cases of recrudescence necessitate evaluation for markers of resistance to detect as early as possible evidence of the occurrence of artemisinin resistance. In the study presented here, a total of 30 cases of LTF were observed from day 21 onwards, giving a rate of re-infection of 24.4 % in the study population. A similarly high re-infection rate following AL treatment was observed in Zambia with 37 % in Chongwe [
29], 20.8 % in Chipata [
29], 30 % in Ndola [
33], and more than 25 % in Burkina Faso [
34]. In Mali [
35] a study on the efficacy and safety of different ACT found more cases of re-infection with AL than with other ACT, such as artesunate–amodiaquine (AS + AQ), artesunate and sulfadoxine–pyrimethamine (AS + SP). These results raise the question of the efficacy of lumefantrine, the long-acting partner drug in the AL combination that should prevent early re-infections. The half-life of artemisinin is approximately 2 h versus four to six days for lumefantrine [
36,
37], which thereby prolongs the antiplasmodial action of the drug combination. Plausibly then, the occurrence of frequent re-infections might indicate a decrease in the sensitivity of some plasmodial strains to lumefantrine. Such results indicate a requirement for regular
in vitro monitoring of the efficacy of lumefantrine on plasmodial strains in countries where the AL combination is used as first-line treatment. The absence of ETF during treatment with AL in this study and in several others [
25,
27,
38,
39] highlights the drug’s efficacy and is emphasized by the rapid rate (48 h) of parasite clearance. These findings are similar to those previously reported in studies from several other countries [
27,
33,
40,
41]. AL clears parasites quickly as a result of the rapidly absorbed, fast-acting artemisinin component. Here, parasite clearance half-lives were around 4 h for most individuals with rapid decline of mean parasitaemia during the first 18 h, results similar to those previously reported in other parts of Africa [
40‐
42]. The difference with the study in Nigeria [
43], where parasitaemia disappeared in all children after 16 h, could be explained by the fact that the study in Nigeria included children aged 12–132 months, i.e., children aged one to 11 years old, many of whom will have developed immunity that can synergize with drugs to promote the rapid elimination of parasites. In this study, having two individuals with delay in clearance half-lives does not undermine the efficacy of AL. According to WHO, partial resistance to artemisinin is suspected when more than 10 % of patients have a parasite clearance half-life longer than 5 h after treatment with ACT [
44].
Rapid fever clearance was noted in all participants, 100 % of whom were fever-free within 24 h. Fever clearance kinetics could also be explained by the fast-acting parasite clearance properties of artemisinins, leading to rapid resolution of symptoms including fever [
45]. An antipyretic (paracetamol) was given to febrile patients, however no patients in the study required paracetamol after 24 h. It is nevertheless important to note that the use of paracetamol should be discussed as a confounding factor contributing to fever clearance time of AL. Other studies have reported similar findings [
25,
26,
33,
46]. Although AL cleared fever and parasitaemia in a very short period of time (less than three days), a concomitant significant increase in the concentration of haemoglobin was not observed. This less-pronounced post-treatment haematological recovery suggests that malaria could be the major contributing factor to the low haemoglobin levels at enrolment, but that the slow rate of recovery may imply that in SSA countries, other factors, such as geohelminths and malnutrition, may play a key role in the occurrence of anaemia as reported in other studies [
40].