Background: Cryptosporidiosis is a worldwide zoonotic parasitic disease found in children and HIV-positive individuals, and is mainly accompanied with diarrhea. Objectives: This study attempted to compare the sensitivity and specificity of acid-fast (AF) staining, polymerase chain reaction (PCR), and enzyme-linked immunosorbent assay (ELISA) methods to determine Cryptosporidium and its predominant species in diarrheal stool samples of children. Methods: In total, 221 diarrheal stool samples were collected from children admitted to Motahari Hospital in Urmia city, NorthWest of Iran. The AF staining and ELISA methods were used to analyze all the samples, while the PCR method was considered as the gold standard of the study. Positive samples shown by PCR were sequenced to determine Cryptosporidium species (spp.). The three methods were compared regarding statistical factors, sensitivity, specificity, positive and negative predictive values, time duration, and experiment costs. Results: Of the 221 analyzed samples, four and seven samples were positive for Cryptosporidium, as indicated by the AF staining and PCR methods, respectively. The sensitivity and specificity of the AF staining method were shown to be 57.14% and 99.53%, respectively, and five out of 94 samples were diagnosed as positive using ELISA (with 71.4% sensitivity and 100% specificity). Conclusions: Our findings showed that ELISA found less false positive and false negative in comparison with the AF staining method to detect Cryptosporidium. Despite having higher sensitivity and specificity in comparison with the ELISA method, PCR needs more time and cost; therefore, ELISA is preferred for laboratory routine works. Due to limited information on molecular epidemiology of Cryptosporidium spp., more studies using molecular methods are needed to elucidate accurate species.