The average temperature in East African countries is estimated to rise by 3-4 °C during the next 70 years due the global warming. Uganda is one of the East African countries which will be greatly affected by the global warming. Due to their vulnerable living conditions, low-income people will be hit the worst by the consequences of climate changes. Around 38% of Uganda’s population live below the international poverty line of $1.25 a day and more than 60% of the country’s urban population live in slums. On the other hand, due to various social and practical reasons, sustainable locally available construction methods and materials, such as adobe and thatched roofs are being gradually replaced with environmentally harmful materials such as concrete and iron sheet roofs. This situation in addition to imminent thermal discomfort caused by the global warming as well as defective design and inappropriate construction methods may considerably affect the health and wellbeing of low-income people the majority of whom live in substandard overcrowded homes. This paper intends to evaluate the effects of different construction methods and materials on the risk of thermal discomfort in low-income houses in Uganda. Dynamic thermal simulations are conducted in EnergyPlus and adaptive model Category II, defined in BS EN 15251, is used for the thermal comfort evaluations. The results reveal that roof construction methods/materials are the key factor in reducing or increasing the risk of thermal discomfort in naturally ventilated buildings in tropical climates. Compared to iron sheet roof, thatched roof provided up to 15 times better conditions by reducing the number of hours during which internal operative temperature exceeded the “limiting maximum acceptable temperature”. Hollow concrete block walls with iron sheet roof was found to be the worst construction method which dramatically failed all three thermal comfort criteria defined by CIBSE TM52.