Objectives - To assess, over a period of 12 months, whether homoeopathic treatment could influence eczema signs/symptoms and quality of life (QoL) compared with conventional treatment.Design - Prospective multi-centre cohort study.Setting - Children with eczema aged 1–16 years were recruited from primary care practices.Interventions - Conventional versus homoeopathic treatment.Outcome measures - Patients (or parents) assessed eczema symptoms by numerical rating scales as well as disease-specific Atopie Lebensqualitaets-Fragebogen (ALF) and general quality of life (KINDL, KITA) at 0, 6 and 12 months.Results - A total of 118 children were included: 54 from homoeopathic (mean age ± S.D. was 5.1 ± 3.3 years; 56% boys) and 64 from conventional practices (6.2 ± 3.8 years; 61% boys). Eczema symptoms (assessed by patients or their parents) improved from 0 to 12 months for both treatment options, but did not differ between the two groups: 3.5–2.5 versus 3.4–2.1; p = 0.447 (adjusted). Disease-related quality of life improved in both groups similarly. In the subgroup of children aged 8–16 years the general quality of life showed a better trend for conventional treatment compared with homoeopathic treatment (p = 0.030).Conclusions - This observational study is the first long-term prospective investigation to compare homoeopathic and conventional treatment of eczema in children. Over a period of 12 months, both therapy groups improved similarly regarding perception of eczema symptoms (assessed by patients or parents) and disease-related quality of life.