Lead (Pb) is a toxic heavy metal that causes physiological and morphological changes in plants. Our current study was aimed at observing Pb-induced changes in seeds of two upland cotton varieties (TM-1 and Z- 747) that were exposed for 24 hours to various Pb concentrations (0, 50, 100, 300, and 500 μM). Seeds of TM-1 showed higher germination percentages, water uptake, and cell viability as compared to Z-747. Changes in nuclei shape, their partial disappearance, and increase in vacuole size were the initial signs of lead toxicity in Z-747, while TM-1 maintained its typical conformations. Cell wall thickening; increase in the number of mitochondria, protein, and lipid bodies; and vacuolation were more prominent in TM-1. In contrast, plasmolytic shrinkage and scattered cell organelles were the key characteristics of Z-747 at higher doses of Pb. Those observations demonstrated that seeds of TM-1 were more tolerant to Pb stress as compared to Z-747 and may be considered a preferred choice for culture on Pb-contaminated soils.