Background: Nephropathy, a vascular complication of hyperglycemia in patients with diabetes mellitus (DM) and prediabetes, is the leading cause of chronic kidney disease. Objectives: This study aimed to investigate the incidence and prevalence of nephropathy and its risk factors in patients with prediabetes, with a particular focus on exploring the association between a family history (FH) of DM and nephropathy. Methods: In this retrospective study, we examined the medical records of 819 patients with prediabetes referred to the Isfahan Endocrine and Metabolism Research Center in 2004. We compared the prevalence of nephropathy in 2019 to baseline levels and assessed factors such as FH of DM in first-degree relatives and other nephropathy-related factors among patients with and without nephropathy. Results: The prevalence of nephropathy increased from 39% to 60.6% over 15 years, with a cumulative incidence of 21.6% and a mean annual incidence of 2.4%. There were differences in diastolic and systolic blood pressure, lipid markers, fasting and postprandial glucose levels, and glomerular filtration rate between patients with and without nephropathy; however, these differences were not statistically significant (P-value ≥ 0.05). Male sex (Odds ratio [OR]: 1.8), age (OR: 1.02), and Body Mass Index (BMI) (OR: 1.05) were significantly associated with nephropathy (P-value < 0.05). No significant association was found between a positive FH of DM and nephropathy (P-value = 0.638). Conclusions: Our findings indicate that a FH of DM is not associated with an increased risk of nephropathy in patients with prediabetes. Instead, sex, age, and BMI play a more significant role. Therefore, these factors may be more critical in guiding preventive and treatment measures.