A cross-sectional survey was conducted to determine the prevalence of Cryptosporidium spp. infection in companion and stray dogs in Kerman, Iran. Faecal samples were randomly collected from 548 dogs (450 companion and 98 stray). Cryptosporidium oocysts were concentrated using the formalin ether sedimentation method according to the modified Ziehl-Neelsen staining technique. Cryptosporidium oocysts were identified in 2% (11/548) of samples. Faeces were classified according to the consistency as diarrhoeic (56/548) and non-diarrhoeic (492/548). Diarrhoea was recorded in 4 of the positive samples (7.14%). The prevalence of cryptosporidiosis was significantly higher in diarrhoeic dogs (7.14%) compared to the non-diarrhoeic dogs (1.4%) (p<0.05). There was no significant difference between the prevalence of Cryptosporidium spp. in stray dogs (4.08%) and companion dogs (1.55%). The age distribution of Cryptosporidium spp. in dogs below 1 year of age had a higher overall prevalence than dogs over 12 months of age (p<0.05). There was no significant difference in the prevalence between male (1.93%) and female (2.1%) dogs. The highest rate of infection was recorded during the autumn (3.9%) but this difference was not statistically significant (p>0.05). This study confirmed that dogs have a potential role in human cryptosporidiosis and faecal examination of dogs with persistent diarrhoea should be performed on a routine basis.