Children are most prone to parasitic infections. The objectives of the study were to examine the occurrence of parasitic infections in children from different populations and to perform molecular characterization of human isolates. We examined 631 stool samples from Roma and non-Roma children for the presence of parasitic developmental stages. Samples were collected from three eastern Slovakia districts. The ages of the children ranged from 1 months to 17 years. Subsequently, the molecular characterization of human isolates by PCR detected triosephosphate isomerase () and beta-giardin () genes was performed. The overall prevalence of parasitic infection was 19.8%. eggs were the most frequent, with an occurrence of about 13.8%. cysts were present in 6.3% of samples. isolates obtained from 13 children were subjected to DNA sequencing with and genes. Five isolates were categorized as bearing subassemblage BIII, the three isolates as subassemblage BIV, one person was infected with a mixture of subassemblages BIII and BIV, four children had subassemblage AII, and one isolate revealed a structure corresponding with subassemblage AI. Our work is proof that poverty and poor hygiene contribute the most to public health problems associated with neglected parasitic diseases.