Background: India contributes the highest share of under-five and neonatal deaths and stillbirths globally. Diagnostic autopsy, although useful for cause of death identification, have limited acceptance. Minimally invasive tissue sampling (MITS) is an alternative to autopsy for identification of the cause of death (CoD). A formative research linked to pilot MITS implementation was conducted to document the perceptions and attitudes of the healthcare professionals and the barriers for implementation. Methods: This exploratory qualitative study conducted at a tertiary care hospital in New Delhi, India included the hospital staffs. In-depth interviews were conducted with the doctors, nurses and support staffs from pediatrics, neonatology, obstetrics and forensic medicine departments. Inductive data analysis was done to identify the emerging themes and codes. Results: A total of 26 interviews (doctors, n = 10; nurses, n = 9 and support staffs, n = 7) were conducted. Almost all professional and support staffs were positive about the MITS and its advantage for CoD identification including co-existing and underlying illnesses. Some opined conduct of MITS for the cases without clear diagnosis. All participants perceived that MITS would be acceptable for parents due to the non-disfigurement and preferred by those who had unexplained child deaths or stillbirths in past. The key factors for MITS acceptance were appropriate communication, trust building, involvement of senior doctors, and engagement of the counselor prior to deaths and training of the personnel. For implementation and sustenance of MITS, involvement of the institute authority and government stakeholders would be essential.