One of the essential steps in targeting tuberculosis (TB) intervention is early diagnosis and treatment of patients by reducing the reservoir of infection in the community. In the North-Eastern (NE) region of India pulmonary TB and paragonimiasis are overlapping public health issues. We performed a cross-sectional study in 63 remote villages from the two states Arunachal Pradesh (AP) and Assam to determine the prevalence of undiagnosed TB and paragonimiasis cases using cough as a simple indicator. In AP, 2961 individuals aged five years and above were examined and 1108 (37·4%) were found to have cough for one week or more. Of the 417 individuals who provided sputum, 11 (2·64%) were smear positive for acid-fast bacilli (AFB). All these cases were yet undiagnosed, thus the prevalence of new smear positive TB in AP was 0·37%. In Assam on the other hand 331 (23·5%) subjects out of 1410 individuals who were examined had a cough for one week or more and of the 112 individuals who provided sputum, 13 (11·6%) were smear positive for AFB. The prevalence of new smear positive TB cases was 0·78% in Assam. Sero-positivity of paragonimiasis in coughers of AP was 7·6% (n = 1091), which was significantly higher (p < 0·01) as compared to that in Assam (1·2%, n = 321). The findings of the present study suggest that TB remains a major public health concern in the NE region of India especially in the remote places and there is need to strengthen early case detection of TB.