Obesity and bariatric surgery have been associated with changes in ventricular function and structure. The aim of the present study was to assess the long-term changes in left ventricular (LV) and right ventricular (RV) function and structure in patients with morbid obesity—body mass index ≥40 kg/m² or ≥35 kg/m² with co-morbidities—who had lost weight after bariatric surgery compared to nonsurgical controls. We reviewed 57 patients with morbid obesity who had undergone gastric bypass surgery and who had undergone echocardiography before and after surgery. A reference group (n = 57) was frequency matched for body mass index (±2 kg/m²), gender, age (±2 years), and follow-up duration (±6 months). After a mean follow-up of 3.6 years, the LV mass and LV mass indexed by height had decreased in the patients who had undergone bariatric surgery and had lost weight. In contrast, these measurements had increased in the patients who had not undergone bariatric surgery. The difference between these 2 groups remained significant after adjusting for potential confounders. At follow-up, neither the patients nor controls showed a significant change in ejection fraction, LV myocardial performance index, or RV myocardial performance index. In the study population as a whole, multivariate analysis showed a positive correlation between the change in body weight and ventricular septum thickness (R = 0.33), posterior wall thickness (R = 0.31), LV mass (R = 0.38), RV end-diastolic area (R = 0.22), and estimated RV systolic pressure (R = 0.39), all with p values <0.05. In conclusion, body weight changes in patients with morbid obesity were associated with changes in LV structure independent of improvement in obesity-related co-morbidities, including obstructive sleep apnea. Weight loss improved the RV end-diastolic area and might prevent progression to RV dysfunction.