BACKGROUND: Remarkable progress has been made in the fight against neglected tropical diseases, but new challenges have emerged. Innovative diagnostics, better drugs and new insecticides are often identified as the priority; however, access to these new tools may not be sufficient to achieve and sustain disease elimination, if certain challenges and priorities are not considered. MAIN BODY: The authors summarise key operational challenges, and based on these, identify two major priorities: strengthening the capacity of the primary health care health system in correctly diagnosing and managing neglected tropical diseases; and establishing an effective disease surveillance process. Five steps are proposed as concrete actions to build an effective primary health care service for neglected tropical diseases, and a health management information system capable of accurately reporting these diseases. Community engagement and formalization of community health workers role are proposed as essential components of these steps. Shift of financial support from disease oriented programmes to disease integrated interventions, improved access to international guidelines for primary health care staff, and availability of donated drugs in health care structures are also suggested as key elements of the proposed process. CONCLUSION: The authors conclude that failure to address these priorities now may lead to further challenges on the long path towards neglected tropical disease elimination and beyond.