BACKGROUND: The Integrated eDiagnosis Approach (IeDA), centred on an electronic Clinical Decision Support System (eCDSS) developed in line with national Integrated Management of Childhood Illness (IMCI) guidelines, was implemented in primary health facilities of two regions of Burkina Faso. An evaluation was performed using a stepped-wedge cluster randomised design with the aim of determining whether the IeDA intervention increased Health Care Workers' (HCW) adherence to the IMCI guidelines. METHODS: Ten randomly selected facilities per district were visited at each step by two trained nurses: One observed under-five consultations and the second conducted a repeat consultation. The primary outcomes were: overall adherence to clinical assessment tasks; overall correct classification ignoring the severity of the classifications; and overall correct prescription according to HCWs' classifications. Statistical comparisons between trial arms were performed on cluster/step-level summaries. RESULTS: On average, 54 and 79% of clinical assessment tasks were observed to be completed by HCWs in the control and intervention districts respectively (cluster-level mean difference = 29.9%; P-value = 0.002). The proportion of children for whom the validation nurses and the HCWs recorded the same classifications (ignoring the severity) was 73 and 79% in the control and intervention districts respectively (cluster-level mean difference = 10.1%; P-value = 0.004). The proportion of children who received correct prescriptions in accordance with HCWs' classifications were similar across arms, 78% in the control arm and 77% in the intervention arm (cluster-level mean difference = - 1.1%; P-value = 0.788). CONCLUSION: The IeDA intervention improved substantially HCWs' adherence to IMCI's clinical assessment tasks, leading to some overall increase in correct classifications but to no overall improvement in correct prescriptions. The largest improvements tended to be observed for less common conditions. For more common conditions, HCWs in the control districts performed relatively well, thus limiting the scope to detect an overall impact. TRIAL REGISTRATION: ClinicalTrials.gov NCT02341469 ; First submitted August 272,014, posted January 19, 2015.