BackgroundMonitoring the progress of the Integrated Disease Surveillance (IDS) strategy is an important component to ensure its sustainability in the state of Maharashtra in India. The purpose of the study was to document the baseline performance of the system on its core and support functions and to understand the challenges for its transition from an externally funded “project” to a state owned surveillance “program”.MethodsMulti-centre, retrospective cross-sectional evaluation study to assess the structure, core and support surveillance functions using modified WHO generic questionnaires. All 34 districts in the state and randomly identified 46 facilities and 25 labs were included in the study.ResultsCase definitions were rarely used at the periphery. Limited laboratory capacity at all levels compromised case and outbreak confirmation. Only 53% districts could confirm all priority diseases. Stool sample processing was the weakest at the periphery. Availability of transport media, trained staff, and rapid diagnostic tests were main challenges at the periphery. Data analysis was weak at both district and facility levels. Outbreak thresholds were better understood at facility level (59%) than at the district (18%). None of the outbreak indicator targets were met and submission of final outbreak report was the weakest. Feedback and training was significantly better (p < 0.0001) at district level (65%; 76%) than at facility level (15%; 37%). Supervision was better at the facility level (37%) than at district (18%) and so were coordination, communication and logistic resources. Contractual part time positions, administrative delays in recruitment, and vacancies (30%) were main human resource issues that hampered system performance.ConclusionsSignificant progress has been made in the core and support surveillance functions in Maharashtra, however some challenges exist. Support functions (laboratory, transport and communication equipment, training, supervision, human and other resources) are particularly weak at the district level. Structural integration and establishing permanent state and district surveillance officer positions will ensure leadership; improve performance; support continuity; and offer sustainability to the program. Institutionalizing the integrated disease surveillance strategy through skills based personnel development and infrastructure strengthening at district levels is the only way to avoid it from ending up isolated! Improving surveillance quality should be the next on agenda for the state.