This study was carried out in Raparin Pediatric hospital in Erbil city. Stool samples (No= 548) were collected from children of less than 1 month to 13 years of age of both genders. The study was designed to assess some immunological parameters with molecular characterization based on sequence analysis of Cryptosporidium spp. positive group compared to the control group. The level of C-reactive protein in cryptosporidiosis positive group showed an extremely significant (p < 0.01) elevation with the mean value of (16.14 ± 3.41) when compared to control group with the mean value of (4.80 ± 1.30). Complement components C3 and C4 showed a significant increase in cryptosporidiosis positive group with mean values of 209.30 ± 36.97 and 1.74 ± 0.016) respectively compared to control group with mean values of 136.00 ± 6.59 and 1.59 ± 0.025 respectively. The results of IgG mean value in the present study showed statistically a non-significant difference among cryptosporidiosis positive group (1751.0 ± 101.5) compared to control group (1586.0 ± 116.0). On the other hand, serum levels of the IgE, IgA and IgM among cryptosporidiosis positive group showed a significant increase (384.0 ± 35.7, 447.0 ± 21.1 and 298.3 ± 16.25) respectively in compared to control group (107.0 ± 24.8, 308 ± 32.9 and 235.2 ± 24.97 respectively). A significant increase (p<0.0001) of IL-18 was observed in cryptosporidiosis positive group (84.11 ± 6.098 ng/L) compared to control group (32.37 ± 4.668 ng/L). A significant increase of TNF-α was observed in cryptosporidiosis positive group (2.68 ± 0.03 ng/L) when compared to control group (2.30 ± 0.06 ng/L).Out of 548 stool samples examined with modified Zhiehl-Neelson (ZN) technique, 59 (10.77%) of them were positive for Cryptosporidium spp. followed by formalin-ether ZN technique with the rate of 10.45% from the total 276 examined stool samples. Then 70 and 21 stool samples with the previously mentioned methods were subjected to immunochromatographic (IC) and PCR-sequence methods respectively and the results showed that the rate 100% of infection with Cryptosporidium spp. for 50 and 15 positive stool samples respectively that previously identified with ZN techniques. On the other hand, 20 and 6 negative samples were obtained for both IC and PCR-sequence methods respectively. The expected amplicon size for CPB-DIAG (18S rDNA) of Cryptosporidium spp. is 450bp, applying molecular procedure based PCR sequencing tool results got from sequencing were only 400 bp (missing 50 bp due to the quality of nucleotide sequence). BLAST program from Genbank was used to compare the results of amplified sequences of the present study with other stored species of Cryptosporidiumsequences. The results indicated that the query sequence was 100% identical to Cryptosporidiumparvum.