Due to its speed, accuracy and cost-effectiveness, microscopy has become an integral part of clinical examination for disease diagnosis. However, modern microscopes are very costly and require skilled personnel for their operation and maintenance, and specimen processing and analysis is labour-intensive. Further, lack of such expensive diagnostic tools in remote areas is a serious concern. Affordable point-of-care diagnostic tools are the most useful for timely disease diagnosis and management. The Foldscope is an affordable origami-based microscopy device composed of a series of paper clippings, which, upon assembly, can hold a specimen slide for observation, and this specimen can be viewed via a mobile phone camera attached to it. The present study evaluated the use of the Foldscope in the clinical diagnosis of oral and urinary tract infections and evaluated its efficacy as a motivational tool for improving oral health among school children in India. We qualitatively compared the Foldscope to a clinical microscope by examining five different types of clinical samples. Of the different types of clinical samples, the Foldscope was effective in detecting infection in dental plaque samples and urine samples. Thus, we further analysed 31 dental plaque samples of patients aged 3-13 years and 25 urine samples of patients aged 11-62 years. We also evaluated the use of the Foldscope as an educational tool for motivating oral hygiene among 80 school children aged 12 years and found that students in the Foldscope intervention group had better measures of oral hygiene than did students in the nonintervention group. In summary, our study indicated that the Foldscope is useful in detecting urinary tract infections and kidney stones in urine samples and is a useful motivational tool for oral health education among school-aged children. Furthermore, it may also be useful in oral health monitoring in resource poor settings. LAY DESCRIPTION: Poor and remote population often suffers due to lack of capacity to buy products or avail services which are expensive. In such a society people are not able to afford even the basic detection of diseases. Foldscope may come to rescue here! Foldscope is a paper-based, use-and-throw, affordable microscope. This study explores the use of Foldscope in clinics and diseases diagnosis using patient samples. Preliminary detection of disease associated symptoms in dental and urinary infections and digital record keeping via storage in mobile phone memory and hospital OPD records for monitoring patient's health are some of the advantages of Foldscope for clinical use in resource poor settings. It identifies that Foldscope not only can be used by students or teachers for educational purposes but it can also pave a path for promotion of dental hygiene among young children. The study also suggests that further improvement in design or resolution of Foldscope will broaden the scope of its application, in future.