Background: Every year, up to three million deaths throughout the world occur as a result of malaria, 90% of which occur in Africa. Despite training providers in malaria case management and the availability of appropriate medical suppliers, there are still weaknesses in the management chain of malaria. Objectives: Our aim was to assess the quality of malaria case management in two primary health care centres in the Goma health district. Specific objectives were the assessment of quality accuracy in the dosage, the duration of treatment, the intervals between administrations, and the routes of administration of anti-malarial medication in two health centres, as well as the subsequent comparison of those two sites. Method: A descriptive retrospective study was conducted using the malaria register's review to assess two health centres in the Goma health district. Socio-demographical and clinical data were recorded and the quality was assessed against the national guidelines. Descriptive statistics with percentages and Chi-square values were computed. Results: Under-dosage was more common in CCLK 9Centre Chretien du Lac Kivu [Lake Kivu Christian Centre]) with 55 patients 962.5%; 95% CI, 52% -71.8%) patients, whilst the over-dosage was present in 64 patients 980%; 95% CI, 69.9% -87.2%) in CASOP 9Caisse de Solidarite Ouvrisre et Paysanne [Fund of Solidarity Workers and Peasants]). The duration of treatment was shorter in CCLK in 15 patients 993.7%; 95% CI, 71.6% -98.8%); CASOP had a high rate of inappropriate intervals between the administration of drugs in 14 patients 982.3%; 95% CI, 58.9% -93.8%). Intravenous administration rates were high in both sites with respectively 102 patients in CASOP 962.5%; 95% CI, 54.9% -69.6%) and 61 patients in CCLK 937.4%; 95% CI, 30.3% -45.0%). Significant differences were found between the two sites with regard to intervals of administration (chi(2) = 7.11, p = 0.007), duration of treatment (chi(2) = 8.51, p = 0.003), dosage (chi(2) = 3.91, p = 0.05). The routes of administration were used in a similar manner, however, in the two sites (chi(2) = 0.78, p = 0.37). Conclusion: Abnormalities in dosage, in the duration of treatment, in the intervals between administration and in the routes of administration were found in both sites. Consequently we conclude that success in guidelines implementation is a complex process and cannot be based only on scientific evidence, but certain contextual factors must be considered.