The objective of this study was to determine the seroprevalence of Neospora caninum, and the effect of associated risk factors in ten sheep production flocks in the state of Colima, Mexico. A total of 350 blood serum samples were collected, processed via the ELISA technique, and risk factors were calculated using logistic regression analysis. The overall prevalence was 13.14%, and 80% of the flocks had at least one positive animal, with a variation from 5.71% to 45.71%. Prevalence was higher in males (18.75%) than in females (12.87%), in purebred animals (13.87%) than in crossbreed animals (11.42%), and in sheep with body condition less than two. Water source, flock size, and the presence of animals other than canines constituted the main risk factors associated with the presence of the disease (P<0.05). In addition, animals raised under an extensive production system tend to present a higher prevalence, while the presence of dogs did not appear to be a risk factor. Animals raised in flocks in which the managers received technical assistance and had more schooling showed 4.12- and 4.15-times higher probability of contracting the disease respectively. The presence of N. caninum in sheep and risk factor identification will allow the development and adoption of good husbandry, as well as proper sanitary and biosecurity practices in order to prevent the transmission of Neospora caninum.