Aim: Hypospadias is a relatively common male genital anomaly that may be caused by anomalies in maternal hormone levels and/or blood glucose levels as well as nutritional deficiencies. Maternal obesity, which increases the risk of diabetes, may alter hormone levels, and may thereby be associated with risk of hypospadias. This study was designed to determine the impact of these risk factors on hypospadias in boys born at the largest tertiary hospital in Qatar. Methods: This population-based, case-control study used linked birth-hospital discharge data from Hamad General Hospital in Doha, Qatar, from January 2007 to December 2012. Boys with hypospadias were identified, and risk factors were determined. Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for hypospadias were estimated by multivariable logistic regression models adjusted for maternal age, parity and body mass index (BMI). Results: Seventy-three newborn male infants with hypospadias and 100 without the condition, with birth weight above 2500 g, were compared. Maternal obesity (BMI ≥ 30 kg/m²) was not associated with risk of hypospadias (aOR 1.07; 95% 0.95 - 1.21), and no trend in risk with increasing maternal BMI was observed. Conclusion: Although the causes of male genital malformation are multifactorial, the present data do not support the hypothesis that gestational maternal obesity is a cause of hypospadias in male infants.