This study aimed to compare the direct immunofluorescence assay (DIF) and the phase contrast microscopy in Sheather solution (PCM) for detection of Cryptosporidium oocysts in fecal samples from calves. The determination of the thresholds of detection of DIF and PCM was performed using five aliquots of a fecal sample from a calf negative for Cryptosporidium spp. oocysts, spiked with different amounts of Cryptosporidium parvum oocysts. The screening of the five aliquots revealed that the DIF and MCF showed respectively, detection thresholds of 3.3x104 (2 positive aliquots) and 3.3x105 (1 positive aliquot) oocysts per gram of fecal sample. Further analyses were accomplished in order to compare the positivity results and to determine semi-quantitatively the number of oocysts per field of microscopy, in both methods, in 300 fecal samples from calves. Among the 300 samples, 19.7% (59/300) were positive by DIF, result that was statistically significant (P=0.0098) when compared with the positivity obtained by the PCM, which was 11.7% (35/300). The positive samples were submitted to the nested-PCR assay for amplification of fragments of the 18S subunit of rRNA, following sequencing of amplified fragments, allowing the identification of Cryptosporidium andersoni in 11.9% (7/59) and C. parvum in 88.1% (52/59) of the samples. The present results indicate that the DIF was more effective than PCM in the detection of Cryptosporidium in fecal samples from calves.