Unacceptable housing conditions prevalent in Indian urban slums adversely affect the health of residents. The Government of India initiated the Basic Services to the Urban Poor (BSUP) as a sub-mission under the Jawaharlal Nehru National Urban Renewal Mission (JNNURM), to provide basic services to the urban poor. As per the available scientific literature, the health effects of such improved housing schemes for the poor have not been studied so far in India, especially in under-five children (0–5 years old) who spend most of their time indoors. The present paper describes the protocol for a follow-up research study proposed to fill this gap. This study, funded by the Indian Council of Medical Research (Sanction No. 5/8-4/9/Env/2020-NCD-II dated 21.09.2021), will be conducted in Bhopal in the central Indian province of Madhya Pradesh for over 2 years. We will recruit 320 under-five children each from Group 1 (Beneficiary families residing in the houses constructed under BSUP) and Group 2 (Slum dwelling families eligible for improved housing but who did not avail of benefit). Eligible children will be recruited in the first household visit. During the same visit, we will record clinical history, examination findings and take anthropometric measurements of participants. We will also collect data regarding socio-economic-environmental parameters of the house. During subsequent monthly follow-up visits, we will collect primary data on morbidity profile, anthropometric details and medical history over 1 year. Approval for the study was obtained from the Institutional Ethics Committee of the National Institute for Research in Environmental Health (No: NIREH/BPL/IEC/2020-21/198, dated 22/06/2020). This study will evaluate the impact of different housing conditions on the health of under-five children. Finding of this research will be beneficial in guiding future housing-related policy decisions in low- and middle-income countries.