Background: Obesity is associated with metabolic syndrome and fat accumulation in various organs such as the liver and the kidneys. Our goal was to assess, using magnetic resonance imaging (MRI) Dual-Echo phase sequencing, the association between liver and kidney fat deposition and their relation to obesity. Methods: We analyzed MRI scans of individuals who were referred to the Chaim Sheba Medical Center between December 2017 and May 2020 to perform a study for any indication. For each individual, we retrieved from the computerized charts data on sex, and age, weight, height, body mass index (BMI), systolic and diastolic blood pressure (BP), and comorbidities (diabetes mellitus, hypertension, dyslipidemia). Results: We screened MRI studies of 399 subjects with a median age of 51 years, 52.4% of whom were women, and a median BMI 24.6 kg/m2. We diagnosed 18% of the participants with fatty liver and 18.6% with fat accumulation in the kidneys (fatty kidneys). Out of the 67 patients with fatty livers, 23 (34.3%) also had fatty kidneys, whereas among the 315 patients without fatty livers, only 48 patients (15.2%) had fatty kidneys (p < 0.01). In comparison to the patients who did not have a fatty liver or fatty kidneys (n = 267), those who had both (n = 23) were more obese, had higher systolic BP, and were more likely to have diabetes mellitus. In comparison to the patients without a fatty liver, those with fatty livers had an adjusted odds ratio of 2.91 (97.5% CI; 1.61–5.25) to have fatty kidneys. In total, 19.6% of the individuals were obese (BMI ≥ 30), and 26.1% had overweight (25 < BMI < 30). The obese and overweight individuals were older and more likely to have diabetes mellitus and hypertension and had higher rates of fatty livers and fatty kidneys. Fat deposition in both the liver and the kidneys was observed in 15.9% of the obese patients, in 8.3% of the overweight patients, and in none of those with normal weight. Obesity was the only risk factor for fatty kidneys and fatty livers, with an adjusted OR of 6.3 (97.5% CI 2.1–18.6). Conclusions: Obesity is a major risk factor for developing a fatty liver and fatty kidneys. Individuals with a fatty liver are more likely to have fatty kidneys. MRI is an accurate modality for diagnosing fatty kidneys. Reviewing MRI scans of any indication should include assessment of fat fractions in the kidneys in addition to that of the liver.