Morbid obesity is a severe chronic disease and subject to surgical methods for losing weight. This intervention is expected to drive to better quality of life and health status. Other important aspects which may be influenced are: HOMA-IR (as insulin resistance marker) and heart rate variability (as cardiac function and autonomic nervous system marker), which are independent and valid predictors of future cardiac, neurological, metabolic health. We pooled 4 studies (646 subjects) resulting to HOMA-IR and nine HRV components-grouped in those undergone to gastric bypass (RYGP) and those operated with vertical sleeve gastrectomy (SG) method. We performed a meta-analysis in patients for HOMA-IR and HRV, using Hedge\'s g correction of Cohen d for small samples. We concluded that RYGP favors insulin resistance decrease, whereas SG increases the vagal tone, improving cardiac function. The severity of cardiovascular diseases history suggests the selection of the surgery method: SG for the most severe cardiovascular cases and RYGP for those with higher HOMA-IR.