BACKGROUND: A national study, 'Costing of healthcare services in India' (CHSI) aimed at generating reliable healthcare cost estimates for health technology assessment and price-setting is being undertaken in India. CHSI sampled 52 public and 40 private hospitals in 13 states and used a mixed micro-costing approach. This paper aims to outline the process, challenges and critical lessons of cost data collection to feed methodological and quality improvement of data collection. METHODS: An exploratory survey with 3 components-an online semi-structured questionnaire, group discussion and review of monitoring data, was conducted amongst CHSI data collection teams. There were qualitative and quantitative components. Difficulty in obtaining individual data was rated on a Likert scale. RESULTS: Mean time taken to complete cost data collection in one department/speciality was 7.86(±0.51) months, majority of which was spent on data entry and data issues resolution. Data collection was most difficult for determination of equipment usage (mean difficulty score 6.59±0.52), consumables prices (6.09±0.58), equipment price(6.05±0.72), and furniture price(5.64±0.68). Human resources, drugs & consumables contributed to 78% of total cost and 31% of data collection time. However, furniture, overheads and equipment consumed 51% of time contributing only 9% of total cost. Seeking multiple permissions, absence of electronic records, multiple sources of data were key challenges causing delays. CONCLUSIONS: Micro-costing is time and resource intensive. Addressing key issues prior to data collection would ease the process of data collection, improve quality of estimates and aid priority setting. Electronic health records and availability of national cost data base would facilitate conducting costing studies.