Cryptosporidium is an intestinal parasite causing cryptosporidiosis, a prevalent diarrheal disease among young children in low- and middle-income countries. This infection causes approximately 48,000 deaths and the loss of 7.9 million disability-adjusted life-years annually. Despite the existence of a low-cost drug, access to treatment is hindered by the limited availability of affordable, straightforward, point-of-care (POC) diagnostic tests. LED microscopy of auramine-phenol (AP) stained fecal smears has demonstrated promising diagnostic accuracy in detecting cryptosporidiosis. In this project, we will implement a test-and-treat strategy in a stepped-wedge cluster randomized trial. The aim is to assess the clinical effectiveness of LED-AP testing, in conjunction with access to targeted drug treatment, in reducing the duration of cryptosporidiosis-induced diarrhea. We will evaluate diagnostic accuracy, operational issues, cost-effectiveness, and test turnaround times in realistic setting in two Sub-Saharan African (SSA) countries. Additionally, we will investigate whether rectal swab samples can expedite test turnaround times compared to bulk stool samples. This project aligns with the UN Sustainable Development Goal 3 and WHO initiatives to reduce the burden of diarrheal diseases. Effective POC diagnostics and treatment are expected to alleviate diarrhea and reduce long-term complications. The findings will be instrumental in updating current diarrheal treatment guidelines, which primarily advocate for syndromic treatment. The outcomes will be of significant interest to health facility staff, ministries of health in SSA, WHO, and the scientific community. This study will provide crucial data on optimizing LED-AP testing to guide clinical decision-making and targeted treatment, thereby preventing the overuse of antibiotics. The introduction of cryptosporidiosis testing can enhance surveillance of this critical pathogen.