Studies with direct measures of body fat distribution are required to explore the association between central and general obesity to cancer risk in postmenopausal women. This study investigates the association between central obesity and general obesity to overall/site-specific cancer risk in postmenopausal women. The analysis included 4,679 Danish postmenopausal women. Body fat distribution was evaluated by whole-body dual-energy X-ray absorptiometry scanners. Cancer diagnoses were extracted from the Danish Cancer Registry and multivariable Cox regression models explored the association between cancer risk and central obesity after adjusting for BMI. Our results showed that high central obese women had a 50% increased risk of overall cancer relative to low central obese women (Q1vs.Q4: [HR:1.50, CI:1.20–1.88]). For site-specific cancers, central obesity was significantly associated with Respiratory (Q1vs.Q4: [HR:2.01, CI:1.17–3.47]), Gastrointestinal (Q1vs.Q4: [HR:1.55, CI:0.99–2.41]) and Female genital organs (Q1vs.Q4: [HR:1.95, CI:1.00–3.78]) cancer diagnoses. Sub-analyses stratified by smoking-habits found a significant association between central obesity and a cancer diagnosis for current (Q1vs.Q4: [HR:1.93, CI:1.25–2.99]) and former smokers (Q1vs.Q4: [HR:1.90, CI:1.23–2.94]). These analyses suggest that central obesity is associated with some cancers in postmenopausal women independent of BMI.