Background: Chronic obstructive pulmonary disease has extrapulmonary manifestations, such as cardiovascular diseases and osteoporosis. The purpose of this research was to determine the relationship between the type and extent of emphysema with thoracic aorta calcification (TAC) and bone mineral density (BMD) at Th4, Th8, and L1 vertebrae. Methods: Emphysema was described by computed tomography parameters (both Fleischner classification and low attenuation value percentage, LAV%) and the clinical FEV1/FVC ratio (Tiffeneau–Pinelli index, TI, TI < 0.7; TI > 0.7). Results: Of 200 included patients (median age 64, 33% women), signs of clinical obstruction (TI) were observed in 104 patients, which had significantly lower BMD and more heavy TAC. BMD correlated negatively with LAV%, Rho = −0.16 to −0.23, while a positive correlation of aortic calcification with LAV% was observed, Rho = 0.30 to 0.33. Multiple linear regression showed that age and TI < 0.7 were independent predictors of BMD, β = −0.20 to −0.40, and β = −0.21 to −0.25; age and hypercholesterolemia were independent predictors of TCA, β = 0.61 and β = 0.19. Conclusions: Clinical TI and morphological LAV% parameters correlated with BMD and TAC, in contrast to Fleischer-graded emphysema, which showed no correlation. However, only TI was an independent predictor of BMD, while the morphologically described type and extent of emphysema could not independently predict any extrapulmonary manifestation.