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Faecal samples from buffalo calves of Jabalpur district were studied from September 2011 to August 2012 using modified Ziehl-Neelsen technique (mZN). An overall positivity of 21.4% was recorded. The prevalence was higher (25.5%) in diarrhoeic as compared to non-diarrhoeic (17.0%) calves. The risk of infection was two times higher in diarrhoeic than non-diarrhoeic calves. As per age, highest prevalence (29.7%) was observed in calves of <1 month and it varied significantly (P<0.05) from >3 months age group. The chances of occurance of Cryptosporidium spp. in calves of <1 month age group was three times higher than >3 month age group. The prevalence in male calves was significantly (P<0.05) higher (32.2%) than female calves (15.9%). The risk was ~3 times higher in male than female. Season wise highest prevalence was observed in winter (30.1%) and lowest in summer (7.94%). The risk of infection was five times higher in winter and four times higher in rainy season as compared to summer. Diarrhoeic faecal samples having mucus (32.8%) showed significantly (P<0.05) higher prevalence than those having blood (7.40%).