Genetic epidemiology faces several challenges: 1. Complexity of Traits: Many diseases are influenced by multiple genes and environmental factors, making it difficult to pinpoint specific genetic causes. 2. Ethical Issues: Genetic research often involves sensitive information that needs to be handled with strict ethical considerations, including issues of privacy and consent. 3. Population Stratification: Differences in allele frequencies between populations can lead to confounding in genetic association studies, requiring careful study design and analysis.