Abstract Background The efficacy of low-dose medicine (LDM) in childhood mild/moderate eczema is not known. We conducted a double-blind, two-stage, randomized, placebo-controlled clinical trial, lasting 23 months, to address this issue. Method Eighty children with chronic mild/moderate eczema were randomly allocated to Group A (placebo) or Group B (treatment group; Galium-Heel®, a low-dose multicomponent medicine based upon natural substances; Guna-Interleukin 12 and Guna-Interferon-γ administered twice a day for six non-consecutive months for each stage). LDM is characterized by the use of biological molecules, such as cytokines, neuropeptides, growth factors, hormones at very low concentrations, which correspond to physiological levels within the human body. The dosage of the cytokines used in this trial (IFN-γ and IL-12) is 10 fg/ml. The SCORAD index was evaluated by the same operator: subjects with a SCORAD index below 20 were considered to have mild eczema (61/80; mean: 10.79), whereas a SCORAD index between 20–50 indicated moderate eczema (19/80; mean: 26.84). The data of 66/80 children were analyzed in stage 1 and those of 62/66 children in stage 2. The primary outcome measure was reduction of eczema severity assessed by the SCORAD index. Secondary outcomes were disease-free interval, and treatment safety and tolerability. Results The decrease in disease severity was greater in Group B than in Group A already in stage 1 (a decrease 63.9% versus 53.2%), but the difference was not significant (p = 0.16). Moreover, subjective symptoms (itching and sleep disturbances) initially decreased and then worsened in Group A, whereas itching decreased linearly and sleep disturbances decreased significantly (p=0.049) in Group B. Conclusions Preliminary evidence suggests potential benefit, but further work is needed to validate this approach. Trial registration The trial was registered with EudraCT number 2010–018640-13 through the database of the National Clinical Trials Monitoring Centre Database (Osservatorio delle Sperimentazioni Cliniche, OsSC) of the Italian Medicines Agency.