BackgroundCryptosporidiosis is a common cause of diarrheal disease in livestock and dogs, and it can result in significant economic losses due to decreased productivity and higher treatment costs. The cryptosporidiosis burden in livestock and dogs is largely unknown and underexploited. We designed a cross-sectional research study to determine the prevalence and factors associated with cryptosporidiosis in livestock and dogs.MethodsThe questionnaire data was downloaded from the Kobotoolbox server in excel format for cleaning and analysis. Laboratory results were matched with the questionnaire data and statistical analysis was performed using STATA version 14 and R version 4.2.2. Descriptive statistics were conducted to determine the frequencies, percentages, and proportions of the different study variables. For the categorical variables, 95% binomial and multinomial confidence intervals were obtained using the commands BinomCI(), with Jeffreys approach, and MultinomCI() available in the DescTools package. To adjust for potential clustering within household, a logistic mixed model approach with household as random effect was chosen and performed using the package glmmTMB. The outcome was a positive or negative test result of each dog. A likelihood ratio test using the lmtest package was used to determine if a predictor was significantly associated with the outcome. To adjust for multiple comparisons, the multcomp package with Tukeys approach was used. First all variables were included in a univariable approach. Second all variables with p-values <0.2 were included in a multivariable model..ResultsDogs were over 50times more likely to have the cryptosporidium infection compared to goat. With aOR 56.07, 95%CI= [10.2569,306.5307] and p-value <0.001. Furthermore, being of Mukonjo tribe was over 20times more likely to have cryptosporidiosis compared to being Musongora. At aOR 24.92, 95%CI= [3.6971,168.0655], p-value 0.0010. Additionally, persons who drunk water from the river ponds were 76.93 times more likely to have cryptosporidium infection compared to the counterparts whose source of drinking water were from protected sources with aOR 76.93, 95% CI= [3.71,1595.324] p-value= 0.0050.ConclusionCryptosporidiosis still remains a big public health problem in Kasese District. Dogs are more at risk of having cryptosporidiosis whereas drinking from river ponds was highly attributed to acquiring cryptosporidiosis.