Genetically modified (GM) crops have revolutionized agriculture for more than two decades. These crops feature genetically engineered plants with improved traits like herbicide and pesticide resistance, enhanced nutritional profiles, and other advantageous characteristics. As of 2024, reports indicated that over 209 million hectares worldwide were planted with various GM crop varieties, such as cotton, canola, soybean, and maize. This widespread adoption of GM crops has sparked global interest and concerns about their safety, sustainability, and ethical implications. However, the World Health Organization (WHO), Food and Agriculture Organization (FAO), Organization for Economic Co-operation and Development (OECD), and Cartagena Protocol on Biosafety have issued guidelines for assessment of traits, allergenicity, toxicity, and its impact on nontarget and beneficial organisms. GM crops have been observed to change the ratio of soil enzymes, especially those involved in the nitrogen and phosphorus cycles. Most case studies involving Glycine max, Oryza sativa, Solanum lycopersicum, and Zea mays shed light on safety assessments of GM crops, revealing potential toxic effects on organs such as the liver, pancreas, kidneys, and reproductive system, along with alterations in hematological, biochemical, and immunologic parameters. Some of these crops may also harbor endotoxins which pose potential risks to human health. Thus, assessing the impact of GM crops goes beyond direct effects on human health and is extended to environmental considerations such as soil microbiota and ecosystem stability. This chapter reviews the methodologies, tools, and regulations involved in assessing these risks through various case studies.