Meiofauna—a collective term to define microscopic animals—represent a numerically important component of biodiversity in most of Earth’s ecosystems and play a crucial role in biogeochemical cycles. Meiofauna have also been used as models to understand fundamental adaptive processes, have contributed to a better understanding of the animal’s Tree of Life, and are believed to be a treasure trove for future genomic studies. To celebrate the diversity of research topics brought to us by the term “meiofauna”, we gathered a multidisciplinary team of 42 ecologists, taxonomists, morphologists, biogeographers, molecular biologists, and scientific disseminators to list 194 fundamental questions in meiofaunal research. Then, through an online survey, 251 scientists, administrators, students, and stakeholders assisted us in reducing this list to 50 top-priority questions. Applied topics related to anthropogenic impact and climate change received the highest scores, whereas questions related to areas in development such as genomics or adaptations, received less attention. Whereas we might not be exploiting meiofauna’s full potential yet, more and more integrative approaches and technological developments will create opportunities to employ these fascinating organisms to answer broad and important questions, despite of their impediments related to their small body size. Meiofauna research agenda should balance amongst investigating general questions, addressing more specialized research topics, and generating primary data on distribution, taxonomy, traits, and DNA sequences. The geographical and taxonomic biases that have historically affected meiofaunal research can be alleviated by promoting international cooperation, open data sharing, and an increase effort in education, taxonomic training, as well as scientific communication. We hope that this will get both researchers and the general public intrigued by those small critters that constantly lurk unseen in front of us.