Fat accumulation in muscle (intermuscular, IM) and viscera plays a role in obesity comorbidities. This study examined the impact of Roux-en-Y gastric bypass (RYGB) surgery in morbid obesity on changes in regional fat and muscle depots, and these body composition markers were correlated with physical function. Women (n = 18) were assessed prior to (baseline) and 12 months following RYGB for regional body composition and physical function. Weight loss from baseline to 12 months was 33.7 (s.e.m. = 1.7)%; total body fat decreased from 86.8 (s.e.m. = 5.8) to 45.8 (s.e.m. = 3.9) kg during follow-up. Differential changes in regional body fat were apparent with a volume loss of 58.4% in visceral fat, 19.8% in abdomen IM fat and 50.7% in thigh IM fat. At baseline, abdomen IM fat volume was related to physical function. There was less loss of abdomen IM fat volume than other depots following surgery; furthermore its relationship with physical function is a novel finding.