Integration of leprosy control into the general health system is an essential element of a leprosy elimination strategy. In India, the process has been undertaken with the assistance of World Bank in a phased manner. In the first phase (2001-2002), 24 low/moderately endemic provinces for leprosy were targeted. Operational research was undertaken in these low/moderate endemic provinces to assess the progress of integration of leprosy control in general health system using defined categories, viz. structural integration, training status, availability of MDT and recording/reporting of cases. Selection of nine provinces, 18 districts, 86 health facilities and 108 sub-centres was performed using multistage stratified random sampling technique. Data were collected by interviewing GHS/vertical staff, scrutiny of records and spot checking of MDT stock by Health officers of three leprosy institutions of the Government of India. The result showed that district leprosy nuclei had formed in 16 of 18 districts. In 56% of health facilities vertical staff were redeployed for delivering general health care. Forty-five percent of medical officers, 71% of health supervisors and 75% of multipurpose workers were trained in leprosy. MDT treatment was available in >80% of health facilities. In only 2% of health facilities 3 months MDT stock of all types was present. Forty-four percent of sub-centres were delivering subsequent doses (second dose onward) of MDT. Reporting through a simplified information system was universal. This study emphasizes the need for reorientation training of Medical Officers, better MDT stock management and decentralized management of cases up to sub-centre level.