We evaluated the importance of body composition, amount of subcutaneous and visceral fat, liver and heart ectopic fat, adipose tissue distribution and cell size as predictors of cardio-metabolic risk in 53 non-obese male individuals. Known family history of type 2 diabetes was identified in 25 individuals. The participants also underwent extensive phenotyping together with measuring different biomarkers and non-targeted serum metabolomics. We used ensemble learning and other machine learning approaches to identify predictors with considerable relative importance and their intricate interactions. Visceral fat and age were strong individual predictors of ectopic fat accumulation in liver and heart along with markers of lipid oxidation and reduced glucose tolerance. Subcutaneous adipose cell size was the strongest individual predictor of whole-body insulin sensitivity and also a marker of visceral and ectopic fat accumulation. The metabolite 3-MOB along with related branched-chain amino acids demonstrated strong predictability for family history of type 2 diabetes. Overweight, obesity and a sedentary life style are major causes of the current global Type 2 diabetes epidemic. Excess body weight promotes insulin resistance and the expanded adipose tissue plays a critical role for this. The subcutaneous adipose tissue is the largest and preferred site to accumulate excess fat but it is limited in its ability to recruit new cells in adults and, thus, cell expansion is the major way of accommodating excess lipids 1,2. Expanded subcutaneous adipose cells tend to become proinflammatory, insulin resistant and to have increased lipolysis. In addition, visceral fat is increasingly used for lipid storage while ectopic fat accumulates in the liver, heart and other tissues, which also enhances insulin resistance and the dysmetabolic state 2,3. Ability to differentiate new subcutaneous adipose cells is reduced in adults with expanded cells, not because of reduced number of precursor cells but as a consequence of increased cell senescence 4. Importantly, individuals with type 2 diabetes (T2D) 5 , and also non-diabetic individuals with family history for T2D (First-Degree Relatives), have inappropriately expanded adipose cells in relation to their BMI 6,7 due to the reduced subcutaneous adipogenesis in the presence of increased senescent progenitor cells 4. Conceptually, there should be a close interaction between ability to store excess lipids in subcutaneous fat and the accumulation of visceral fat, ectopic fat and development of a dysmetabolic state. The associations and potential regulation exercised by subcutaneous adipose tissue lipid accumulation and cellular morphology on overall metabolic risk profile with imaging and metabolomics data and relation to family history have, to our knowledge, never been examined before in man.