Background: Intestinal parasitic infections continue to be a significant public health issue in school-aged children, especially in settings of low sanitation standards, unsafe water and poor hygiene. These infections can not only have gastrointestinal effects but can also impact on haematological status, iron metabolism and inflammatory processes. Studies available, however, tend to concentrate on prevalence and fewer studies explore the link between intestinal parasites and relevant clinically important biomarkers. Aim: The purpose of this study was to assess the relationship between intestinal parasitic infection and the blood, iron status and inflammatory markers among school-aged children in the diagnosis which was not based on non-PCR techniques. The objective of this study was to use strengthened non-PCR diagnostic techniques to examine the correlation between intestinal parasitic infection and some blood markers, iron status and inflammatory markers in the study of school-age children. Methods: The study was a comparative cross-sectional study that included 280 school-aged children aged 6–12 years. Direct saline wet mount, iodine wet mount, formalin-ethyl acetate concentration, trichrome staining, modified Ziehl-Neelsen staining, Kato-Katz technique, cellophane tape test and some stool antigen tests were used. CBC, red cell indices, eosinophils, platelets, serum iron, ferritin, total iron-binding capacity, transferrin saturation, C-reactive protein, erythrocyte sedimentation rate and total IgE were measured in blood samples. Fecal calprotectin was used as an indicator of intestinal inflammation. Participants were grouped into parasite-negative, protozoa-positive, helminth-positive and mixed-infection groups. Results: 42.1% of all subjects had an intestinal parasitic infection. The most common type of infection was protozoal and Giardia duodenalis was the most frequently detected parasite. The mean of all the parameters (haemoglobin, haematocrit, MCV, MCH, serum iron and transferrin saturation) were significantly lower in parasite positive children than in parasite negative children. Children with infection, however, had significantly elevated RDW, WBC count, eosinophils, platelets, CRP, ESR, total IgE and faecal calprotectin. The greatest changes in biomarkers were observed with mixed infections and heavy parasite levels. Untreated drinking water, handwashing less often than weekly, eating unwashed vegetables, biting nails, and touching animals were all independent risk factors for infection, as was rural living. Conclusion: Hematological, iron status and inflammatory biomarker changes were highly associated with intestinal parasitic infections in school-aged children. The results suggest the following: The use of integrated non-PCR parasitological diagnosis, in combination with the use of biomarkers, for better assessment of the clinical impact of intestinal parasites in children.