The aim of this field study was to determine the efficacy of vaccination against highly pathogenic avian influenza (HPAI) virus strain H5N1 in Indonesia. A limited, prototype clinical trial was performed using a standardised treatment group, in which poultry flocks were vaccinated at least twice with a selected H5N1 vaccine, and a control group comprising flocks treated with nonstandardised procedures chosen by the farmer. Each group consisted of six flocks comprising either layers or native chickens. Haemagglutination inhibition (HI) antibody levels were determined by regular serum sampling, and outbreak surveillance relied on non-AI-vaccinated sentinel birds. After three vaccinations high antibody titres were produced in the treatment group, and the percentage of layers with an HI titre > 40 was approximately 90%. Although no conclusions can be drawn regarding reduction of virus transmission, this study demonstrated that 11 farms remained free from AI during the observation period, and that a surveillance programme based on differentiating infected from vaccinated animals (DIVA) can be implemented.