Effort of reducing CO2 emissions in developing countries may require an increasing utilization of biomass fuels. Biomass pellets seem well-suited for residential biomass markets. However, there is limited quantitative information on pollutant emissions from biomass pellets burning, especially those measured in real applications. In this study, biomass pellets and raw biomass fuels were burned in a pellet burner and a conventional stove respectively, in rural households, and metal emissions were determined. Results showed that the emission factors (EFs) ranged 3.20–5.57 (Pb), 5.20–7.58 (Cu), 0.11–0.23 (Cd), 12.67–39.00 (As), 0.59–1.31 mg/kg (Ni) for pellets, and 0.73–1.34 (Pb), 0.92–4.48 (Cu), 0.08–0.14 (Cd), 7.29–13.22 (As), 0.28–0.62 (Ni) mg/kg for raw biomass. For unit energy delivered to cooking vessels, the EFs ranged 0.42–0.77 (Pb), 0.79–1.16 (Cu), 0.01–0.03 (Cd), 1.93–5.09 (As), 0.08–0.19 mg/MJ (Ni) for pellets, and 0.30–0.56 (Pb), 0.41–1.86 (Cu), 0.04–0.06 (Cd), 3.25–5.49 (As), 0.12–0.26 (Ni) mg/MJ for raw biomass. This study found that moisture, volatile matter and modified combustion efficiency were the important factors affecting metal emissions. Comparisons of the mass-based and task-based EFs found that biomass pellets produced higher metal emissions than the same amount of raw biomass. However, metal emissions from pellets were not higher in terms of unit energy delivered.