Background Childhood cancer is one of the primary causes of disease‐related death in 5‐ to 14‐year‐old children and currently no prevention strategies exist to reduce the incidence of this disease. Childhood cancer has a larger hereditary component compared with cancer in adults. Few genetic studies have been conducted on children with cancer. Additionally, Latin American populations are underrepresented in genomic studies compared with other populations. Therefore, the aim of this study is to analyze germline mutations in a group of mixed‐ancestry Mexican pediatric patients with solid and hematological cancers. Methods We analyzed genetic variants from 40 Mexican childhood cancer patients and their relatives. DNA from saliva or blood samples was used for whole‐exome sequencing. All variants were identified following GATK best practices. Results We found that six patients (15%) were carriers of germline mutations in CDKN2A, CHEK2, DICER1, FANCA, MSH6, MUTYH, NF1, and SBDS cancer predisposition genes, and additional new variants predicted to be deleterious by in silico algorithms. A population genetics analysis detected five components consistent with the demographic models assumed for modern mixed‐ancestry Mexicans. Conclusions This report identifies potential genetic risk factors and provides a better understanding of the underlying mechanisms of childhood cancer in this population. We found that 15% of confirmed mixed‐ancestry Mexican patients were carriers of germline mutations in CDKN2A, CHEK2, DICER1, FANCA, MSH6, MUTYH, NF1, and SBDS. This first report identifies potential genetic risk factors and provides a better understanding of the underlying mechanisms of childhood cancer in this population.