Gut microbiota is dominated by bacteria; however, fungi species account for approximately 0.01 % to 0.1 % of metagenomic reads from adult stool samples [1], [2], [3]. Despite this small percentage, fungi interact with the immune system and maintain health [4], [5], [6]. However, fungi are also well-known causes of human disease [7]. Alteration of the gut fungal composition (fungal dysbiosis) has been associated with immune-mediated diseases such as inflammatory bowel diseases [8], [9] and celiac disease in different populations from different geographical areas [10], [11], [12], [13], [14]. Studies describing the mycobiome in the gut are primarily from adults in Western countries and information from other geographic areas, where the population has different cultural and dietary lifestyles are scarce. Therefore, the objective of this report was to describe the profile of fungi in fecal samples from healthy Saudi children, a Middle Eastern population with cultural and dietary lifestyle different from Western populations.