Background G. intestinalis and Cryptosporidium spp. are responsible for gastrointestinal infections worldwide. Contaminated food, feces, drinking water and predictors such as poverty, cultural and behavioral aspects have been involved in their transmission. Published studies about these infections are limited in Mexico. Cananea, Sonora is located in northwest Mexico and is one of the regions with the lowest marginalization index in the Sonora state. However, its rate of gastrointestinal infections increased from 48.7/1000 in 2003 to 77.9/1000 in 2010 in the general population. It was estimated that the prevalence of giardiasis can range from 20 to 30% in the Sonoran childhood population. However, the prevalence of giardiasis and cryptosporidiosis are unknown in Cananea, Sonora and they are likely contributing to its gastrointestinal infections rates.MethodsA total of 173 children (average age 8.8 ± 2.8 years) participated in this cross-sectional study. Anthropometric measurements and stool analysis were performed. Socioeconomic, cultural and symptomatology information were collected. The association between the risk factors and intestinal parasitic infections was analyzed by multivariate analysis using the STATA/SE package at a significance level of p ≤ 0.05.ResultsMore than half of the children (n = 103, 60%) had intestinal parasitic infections. Cryptosporidium spp. showed the highest prevalence (n = 47, 27%), which was followed by G. intestinalis (n = 40, 23%). Children with giardiasis and cryptosporidiosis had lower H/A and BMI/A Z scores than children who were free of these infections. Children with giardiasis were at higher risk (OR = 4.0; 95%CI = 1.11–13.02; p = 0.030) of reporting abdominal pain, and children who drank tap water were at higher risk (OR = 5.0; 95% CI = 1.41–17.20; p = 0.012) of cryptosporidiosis.ConclusionsThis was the first epidemiological study conducted in children in the region of Cananea, Sonora in northwest Mexico. The findings revealed a high prevalence of cryptosporidiosis and giardiasis, and their interactions with multiple risk factors were investigated. This study suggested that giardiasis and cryptosporidiosis may play an important role as causative factors of gastrointestinal diseases in the study region. Regional authorities must analyze water for human consumption to search for Cryptosporidium spp. and G. intestinalis.