Abstract Objectives The aim of this study was to compare the diagnostic sensitivity and specificity of the modified Kinyoun's acid-fast test used widely in Saudi Arabia compared to the direct immunofluorscent assay (DFA) for monitoring the occurrence of Cryptosporidium spp. Methods We compared the conventional, modified Kinyoun's acid-fast with the Merifluor direct immunofluorscent assay for the detection of Cryptosporidium oocysts in 100 stool samples, among patients who reported to King Fahad Military Medical Complex during April–May, 2012. Results The modified Kinyoun's method and the DFA revealed 49 and 66 Cryptosporidium oocyst positives, respectively. Sensitivity and specificity of acid-fast when compared to DFA, were 66.67% (95% CI: 53.99%–77.79%) and 88.24% (95% CI: 72.53%–96.63%), respectively, (Kappa = 0.487 and the 95% confidence interval was 0.328–0.645). The positive and negative predictive values of the same method were 91.67% (95% CI: 80.00%–97.63% and 57.69% (95% CI: 43.21%–71.27%), respectively. Conclusion The DFA was found to be simple to perform and has been demonstrated to have a higher sensitivity than traditional staining procedures. The current positivity rate of 66% of Cryptosporidium in this study is higher than indicated before by several studies. This disease remains underdiagnosed in current routine laboratory procedures. It is recommended that tests for Cryptosporidium be done as part of a general diarrhea screen during standard stool tests in diagnostic laboratories.