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BACKGROUND: Government of India is introducing new and relatively costly vaccines under immunization program. Monitoring of vaccine wastage is needed to guide the program implementation and forecasting. Under pilot introduction of rotavirus vaccine in two districts both 5- and 10-doses vials were used, which was considered as an opportunity for documenting the wastage. The wastage rates for other routine vaccines were also documented. METHODS: A survey conducted in two districts (Kangra, Himachal Pradesh and Pune, Maharashtra) covered 49 vaccine stores, 34 sub-centres and 34 outreach sessions collected vaccine receipt, distribution and usage data for two complete years 2016 and 2017. RESULTS: The overall wastage rates for almost all vaccines were higher in Kangra district (BCG 37.1%, DPT 32.1%, Measles 32.2%, OPV 50.8%, TT 34.1% and pentavalent 18.4%) than Pune district (BCG 35.1%, DPT 25.4%, Measles 21.7%, OPV 14.3%, TT 23.1% and pentavalent 13.2%). Wastage for pneumococcal conjugate and measles-rubella vaccines in Kangra district were 27 and 40.5%, respectively. With transition from 5- to 10-doses vials for rotavirus vaccine, wastage at stores levels increased in both Kangra (29 to 33.2%) and Pune (17.8 to 25.7%) districts. With transition from intramuscular to intradermal fractional inactivated polio vaccine, the wastage increased from 36.1 to 54.8% in Kangra and 18.4 to 26.9% in Pune district. CONCLUSIONS: The observed vaccine wastage rates for several vaccines were relatively higher than program assumption for forecasting. The observed variations in the vaccine wastage indicates need for state or region based documentation and monitoring in India for appropriate programmatic action.