We present a novel semi-supervised multimodal relevance vector regression (SM-RVR) method for predicting clinical scores of neurological diseases from multimodal brain images, to help evaluate pathological stage and predict future progression of diseases, e.g., Alzheimer’s diseases (AD). Different from most existing methods, we predict clinical scores from multimodal (imaging and biological) biomarkers, including MRI, FDG-PET, and CSF. Also, since mild cognitive impairment (MCI) subjects generally contain more noises in their clinical scores compared to AD and healthy control (HC) subjects, we use only their multimodal data (i.e., MRI, FDG-PET and CSF), not their clinical scores, to train a semi-supervised model for enhancing the estimation of clinical scores for AD and healthy control (HC). Experimental results on ADNI dataset validate the efficacy of the proposed method.