Summary Background Parkinson’s disease is associated with an increased incidence of cognitive impairment and dementia. Predicting who is at risk of cognitive decline early in the disease course has implications for clinical prognosis and for stratification of participants in clinical trials. We assessed the use of clinical information and biomarkers as predictive factors for cognitive decline in patients with newly diagnosed Parkinson’s disease. Methods The Parkinson’s Progression Markers Initiative (PPMI) study is a cohort study in patients with newly diagnosed Parkinson’s disease. We evaluated cognitive performance (Montreal Cognitive Assessment [MoCA] scores), demographic and clinical data, APOE status, and biomarkers (CSF and dopamine transporter [DAT] imaging results). Using change in MoCA scores over 2 years, MoCA scores at 2 years’ follow-up, and a diagnosis of cognitive impairment (combined mild cognitive impairment or dementia) at 2 years as outcome measures, we assessed the predictive values of baseline clinical variables and separate or combined additions of APOE status, DAT imaging, and CSF biomarkers. We did univariate and multivariate linear analyses with MoCA change scores between baseline and 2 years, and with MoCA scores at 2 years as dependent variables, using backwards linear regression analysis. Additionally, we constructed a prediction model for diagnosis of cognitive impairment using logistic regression analysis. Findings 390 patients with Parkinson’s disease recruited between July 1, 2010, and May 31, 2013, and for whom data on MoCA scores at baseline and 2 years were available. In multivariate analyses, baseline age, University of Pennsylvania Smell Inventory Test (UPSIT) scores, CSF amyloid β (Aβ42) to t-tau ratio, and APOE status were associated with change in MoCA scores over time. Baseline age, MoCA and UPSIT scores, and CSF Aβ42 to t-tau ratio were associated with MoCA score at 2 years (using a backwards p-removal threshold of 0·1). Accuracy of prediction of cognitive impairment using age alone (area under the curve 0·68, 95% CI 0·60–0·76) significantly improved by addition of clinical scores (UPSIT, Rapid Eye Movement Sleep Behaviour Disorder Screening Questionnaire [RBDSQ], Geriatric Depression Scale, and Movement Disorder Society Unified Parkinson’s Disease Rating Scale motor scores; 0·76, 0·68–0·83), CSF variables (0·74, 0·68–0·81), or DAT imaging results (0·76, 0·68–0·83). In combination, the five variables showing the most significant associations with cognitive impairment (age, UPSIT, RBDSQ, CSF Aβ42, and caudate uptake on DAT imaging) allowed prediction of cognitive impairment at 2 years (0·80, 0·74–0·87; p=0·0003 compared to age alone). Interpretation In newly diagnosed Parkinson’s disease, the occurrence of cognitive impairment at 2 year follow-up can be predicted with good accuracy using a model combining information on age, non-motor assessments, DAT imaging, and CSF biomarkers.