Background: In this paper, we aimed to investigate the potential impacts of a fire accident in a fertilizer warehouse on chromosomal anomalies, including Trisomy 21 (T21) and Trisomy (T18) among pregnancies in Brazos County, Texas. We conducted an observational study in Brazos County, TX, with all patients of T18 and T21 cases in the live births in Brazos County between 2005–2014. The prevalence of T18 and T21 before, during, and after the accident in Brazos County were calculated and compared. The Standardized Morbidity Ratio (SMR) was applied to compare the prevalence of T18 and T21 in Brazos County to the statewide prevalence in Texas after adjusting for maternal race and age. Compared with statewide risk, the risk of T18 during the impacted years in Brazos county was found to be significantly higher (SMR = 5.0, 95% Confidence Interval(CI): 2.19–9.89), while there was no significant difference before (SMR = 0.77, 0.13–2.54) and after the accident (SMR = 0.71, 0.12–2.36). However, the prevalence of T21 during the impacted years was not significantly different from those before or after the accident. This study conclusively suggests that this fertilizer fire may be related to the increased prevalence of T18 in Brazos County, though the findings warrant further investigation.