In sub-Saharan Africa, biomass fuels account for approximately 90% of household energy consumption. Limited evidence exists on the association between different biomass fuels and health outcomes. We report results from a cross-sectional sample of 655 households in Malawi. We calculated odds ratios between hypothesized determinants of household air pollution (HAP) exposure (fuel, stove type, and cooking location) and five categories of health outcomes (cardiopulmonary, respiratory, neurologic, eye health, and burns). Reliance on high- or low-quality firewood or crop residue (vs. charcoal) was associated with significantly higher odds of shortness of breath, difficulty breathing, chest pains, night phlegm, forgetfulness, dizziness, and dry irritated eyes. Use of high-quality firewood was associated with significantly lower odds of persistent phlegm. Cooks in rural areas (vs. urban areas) had significantly higher odds of experiencing shortness of breath, persistent cough, and phlegm, but significantly lower odds of phlegm, forgetfulness, and burns. With deforestation and population pressures increasing reliance on low-quality biomass fuels, prevalence of HAP-related cardiopulmonary and neurologic symptoms will likely increase among cooks. Short- to medium-term strategies are needed to secure access to high-quality biomass fuels given limited potential for scalable transitions to modern energy.