Faecal samples were collected from 338 less than 03 month-old dairy calves from 34 cattle herds located in three regions of northeastern Algeria in order to characterize Cryptosporidium oocyst output using Ziehl-Neelsen, Heine and immunofluorescence methods and to identify different species of Cryptosporidium using a PCR 18S. Faecal samples were processed, firstly, through concentration and modified Ziehl-Neelsen staining techniques. Then, 93 faecal samples (not concentrated) were randomly selected and analyzed with the Heine staining technique. Positives samples revealed by both methods, Heine and Ziehl-Neelsen, were analyzed by direct immunofluorescent antibody test and by PCR 18S. Twenty-three herds out of thirty four (68%) were found positive and 108 (32%) calves were shedding oocysts. The prevalence of excretion peaked when calves were 15-30 days of age. However, it was found that the majority of infected calves were coupled to diarrhoea in 1-14 day old calves. Moreover, calves aged 1-14 days showed a higher level of oocyst shedding with OPG equal to 5.2× 104. Three species were identified by sequencing of the 18S PCR products; Cryptosporidium parvum, Cryptosporidium bovis and Cryptosporidium andersoni. These results represent the first report on the genetic identification of Cryptosporidium species in dairy cattle in Algeria and confirm the frequent occurrence of Cryptosporidium in diarrhoeic calves.