Giardia intestinalis and Blastocystis hominis cause frequent infections in children in developing countries. However, the role of intestinal inflammation in their pathogenesis is still poorly understood. Faecal calprotectin (FC) level is used as an indicator of intestinal inflammation and neutrophil migration in the intestinal tract. The present study aimed to evaluate intestinal inflammation by measuring FC level among children infected with either G. intestinalis or B. hominis before and after treatment. Stool samples were collected from 282 children inhabiting a rural area in Egypt and examined microscopically for intestinal parasites. FC level was estimated in a group of children infected with G. intestinalis (n = 12) or B. hominis (n = 12) before and 3weeks after receiving nitazoxanide (200mg twice daily for 3days) and compared to a control group (n = 18) of parasite-free children. Cases of mixed infection were excluded. Nitazoxanide cure rate was 83% in both infections with a remarkable reduction of infection intensity in uncured children. The difference in FC levels between infected children and controls was not statistically significant. Also, the difference between the pre- and post-treatment estimations was not statistically significant. Elevated levels were observed before treatment in three children (two infected with G. intestinalis and one with B. hominis) who displayed normal post-treatment levels. Although G. intestinalis and B. hominis infections appear to cause no remarkable intestinal inflammation, they may induce abnormally elevated FC levels in a subset of children.