The increasing availability of multimodal data from electronic health records (EHR) has paved the way for deep learning methods to improve diagnosis accuracy. However, deep learning models are data-driven, requiring large-scale datasets to achieve high generalizability. Inspired by how human experts leverage reasoning for medical diagnosis, we propose CARER, a novel health risk prediction framework, that enhances deep learning models with clinical rationales derived from medically proficient Large Language Models (LLMs). In addition, we provide a cross-view alignment loss which aligns the “local” view from the patient’s health status with the “global” view from the external LLM’s clinical reasoning to boost the mutual feature learning. Through extensive experiments on two predictive tasks using two popular EHR datasets, our CARER’s significantly exceeds the performance of state-of-the-art models by up to 11.2%, especially in improving data efficiency and generalizability. Our code is available at https://github.com/tuandung2812/CARER-EMNLP-2024