The pathogenic potential and genetic diversity of Blastocystis are poorly understood despite being one of the most frequent intestinal parasites in routine fecal examination all around the world as well as Turkey. There are numerous defined subtypes (ST) of Blastocystis which infect animals and nine of them were isolated from human fecal samples. Blastocystis is an anaerobic parasite and generally recognized as nonpathogenic microorganism that colonizes the colon. However recent studies have indicated that the genotypes may be related with the pathogenicity and clinical symptoms of the infection. The aims of this study were to investigate the subtypes of Blastocystis isolates obtained from stool samples submitted to the parasitology laboratory of Adnan Menderes University, Faculty of Medicine, and to evaluate the clinical symptoms of infected cases. A total of 61 cases (40 male, 21 female; age range: 5-69 years, mean age: 35 ± 19.1 years) were included in the study. Stool samples that were positive for Blastocystis cysts in direct microscopic examination, were inoculated in Jones medium and incubated at 37°C for 72 hours for the growth of parasite. Genomic DNAs were isolated from Jones medium directly or frozen samples with a commercial kit (DNAzol, Invitrogen, USA). The subtypes of Blastocystis were detected by polymerase chain reaction (PCR) using ST-specific primers and the symptoms of patients were evaluated retrospectively. Forty-four (72.1%) out of 61 isolates were subtyped by PCR, while 17 (27.9%) could not be typed. The distribution of Blastocystis subtypes were found as follows; ST3 in 17 (38.6%), ST2 in 13 (29.5%), ST1 in 9 (20.5%), ST1 + ST3 in 4 (9.1%), and ST1 + ST2 in one (2.3%) of the samples. The most common symptoms among Blastocystis infected cases were abdominal pain (n= 24, 39.4%), pruritus (n= 22, 36.1%), diarrhea (n= 4, 6.6%) and constipation (n= 2, 3.3%), respectively. This is the first study investigating the genotypes of Blastocystis in Aydin province (located at Aegean region of Turkey), and the findings were consistent with those reported from other regions. The predominant subtype was found as ST3, like other studies in our country and this data supports that ST3 is a human originated genotype of Blastocystis. Additionally, the higher rate of pruritus detected among our patients infected with Blastocystis compared with the other studies was considered remarkable. In conclusion, multicenter and large-scaled molecular and clinical studies are needed to elucidate the pathogenicity and the epidemiology of Blastocystis infections.