Cryptosporidiosis is a disease caused by the Cryptosporidium spp parasite. As some species of Cryptosporidium have a wide host spectrum, the characterization of the pathogen at the species or genotype level is of great importance to define the sources of infection for humans and the potential for public health. This study investigated the diversity of the genus Cryptosporidium spp. in humans from all over the American continent and observed whether the method used to search for the parasite influenced the prevalence found in the Americas. This systematic review was carried out using the Pubmed, Science direct, Lilacs, Scielo, and Scopus databases with publications from January 1, 2010, to December 31, 2020. For data synthesis, the PRISMA flowchart was used and for the meta-analysis we used the MetaXL program. Of the selected publications, 57, 9 and 16 belonged to the region of South, Central and North America, respectively. The prevalence found for South, Central, and North America was 7%, 7%, and 8%, respectively, when analyzing publications that used only the microscopy method. When we analyzed the publications that used immunological and molecular methods, we found prevalences of 10%, 9%, and 21% for South, Central, and North America, respectively. The C. hominis subtype IbA10G2 was the most reported in the American continent, followed by subtype IeA11G3T3 and, for C. parvum, subtype IIaA15G2RI was the most reported. In conclusion, Cryptosporidium spp. is present throughout the American continent and its prevalence is higher when immunological and/or molecular methods are used, in addition to direct microscopic examination.