Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic kidney disease. Patients at high risk of severe disease progression should be identified early in order to intervene with supportive and therapeutic measures. However, the glomerular filtration rate (GFR) may remain within normal limits for decades until decline begins, making it a late indicator of rapid progression. Kidney volumetry is frequently used in clinical practice to allow for an assessment of disease severity. Due to limited prognostic accuracy, additional imaging markers are of high interest to improve outcome prediction in ADPKD, but data from clinical cohorts are still limited. In this study, we examined cyst fraction as one of these parameters in a cohort of 142 ADPKD patients. A subset of 61 patients received MRIs in two consecutive years to assess longitudinal changes. All MRIs were analyzed by segmentation and volumetry of the kidneys followed by determination of cyst fraction. As expected, both total kidney volume (TKV) and cyst fraction correlated with estimated GFR (eGFR), but cyst fraction showed a higher R2 in a univariate linear regression. Besides, only cyst fraction remained statistically significant in a multiple linear regression including both htTKV and cyst fraction to predict eGFR. Consequently, this study underlines the potential of cyst fraction in ADPKD and encourages prospective clinical trials examining its predictive value in combination with other biomarkers to predict future eGFR decline.