The widespread presence of overweight and obesity increases with every decade, and the number of people with body mass index (BMI) >30 kg/m2 has doubled in the last 30 years. The aim of the study is to assess the correlation between MRI-evaluated ectopic fat accumulation in pancreas, skeletal muscles and liver and the incidence of type 2 diabetes and hypertension, depending on BMI and waist circumference ratio. This prospective study included 267 consecutive patients who were referred to abdominal MRI and underwent a standard clinical assessment with BMI and waist circumference ratio calculation. Ectopic fat accumulation in pancreas, skeletal muscles and liver was evaluated in magnetic resonance imaging using the fat-water separated Dixon imaging. There were statistically significant differences in mean steatosis of all assessed organs in the group of patients with type 2 diabetes or hypertension in comparison to the non-diabetic group as well as to the group without hypertension. It has been observed that pancreas and skeletal muscles are more susceptible to fat accumulation than liver. According to our results, there is a relation between the fat content in muscles, pancreas and liver, the incidence of type 2 diabetes and hypertension and also body mass index and waist circumference ratio. We believe that future studies should aim to determine whether the use of fat content measurement in certain organs could be used as a biomarker that can enable early detection of reversible metabolic changes, as well as their subsequent monitoring.