In acute gastroenteritis (GE), identification of the infectious agent is important for patient management and surveillance. The prevalence of GE caused by protozoa may be underestimated in Swedish patients. The purpose was to compare the prevalence ofE. histolytica,Cryptosporidiumspp.,G. intestinalis, andC. cayetanensisin samples from patients where the clinician had requested testing for gastrointestinal parasites only (n = 758) to where testing for bacterial GE only (n = 803) or where both parasite and bacterial testing (n = 1259) was requested and a healthy control group (n = 197). This prospective cohort study was conducted in Region Jonkoping County, Sweden (October 2018-March 2019). Fecal samples were analyzed with microscopy and real-time PCR.Cryptosporidiumspp. was detected in 16 patients in the bacterial GE group and in 13 in the both bacterial and parasite group; no cases were detected in the group were only parasite infection was suspected.C. cayetanensiswas detected in two patients in the bacterial GE group. One case ofE. histolyticawas detected in the bacterial group and one in the both bacterial and parasite group.G. intestinaliswas detected in 14 patients in the parasite only group, 12 in the both parasite and bacterial group, three in the bacterial GE group, and one in the control group. Diarrhea caused by protozoa, especially Cryptosporidium was under-recognized by clinicians and is likely more common than hitherto estimated in Sweden. A more symptom-based diagnostic algorithm may increase detection and knowledge about protozoan infections.