Based on the widespread use of homeopathy in treatment of animal disease and the poor documentation of its possible effects and consequences, a clinical trial was carried out in order to evaluate the efficacy of homeopathy in treatment of clinical mastitis in dairy cows and a design for clinical studies on homeopathic treatment, taking into account the guidelines for randomized-clinical trials (RCT) as well as the basic principles of homeopathy. A three-armed, stratified, semi-crossover design comparing homeopathy, placebo and a standardized antibiotic treatment was used. Fifty-seven dairy cows were included. Evaluation was made by two score scales, with score I measuring acute symptoms and score II measuring chronic symptoms, and by recording the frequencies of responders to treatment based on four different responder definitions. Significant reductions in mastitis signs were observed in all treatment groups. Homeopathic treatment was not statistically different from either placebo or antibiotic treatment at day 7 (P = 0.56, P = 0.09) or at day 28 (P = 0.07, P = 0.35). The antibiotic treatment was significantly better than placebo measured by the reduction in score I (P < 0.01). Two-thirds of the cases both in the homeopathy and placebo groups responded clinically within 7 days. The outcome measured by frequencies of responders at day 28 was poor in all treatment groups. Evidence of efficacy of homeopathic treatment beyond placebo was not found in this study, but the design can be useful in subsequent larger trials on individualized homeopathic treatment.