We aim to develop a retrieval-augmented generation (RAG) framework capable of answering questions over a corpus of visually-rich documents presented in mixed modalities (e.g., charts, tables) and diverse formats (e.g., PDF, PPTX). In this paper, we present a new RAG framework, VDocRAG, which can directly understand varied documents and modalities in a unified image format to prevent missing information that occurs by parsing documents to obtain text. To improve the performance of VDocRAG, we propose novel self-supervised pre-training tasks that adapt large vision-language models for retrieval by compressing visual information into dense token representations while aligning them with textual content in documents. Furthermore, we introduce OpenDocVQA, the first unified collection of open-domain document visual question answering datasets, encompassing diverse document types and formats. OpenDocVQA provides a comprehensive resource for training and evaluating retrieval and question answering models on visually-rich documents in an open-domain setting. Experiments show that VDocRAG substantially outperforms conventional text-based RAG and has strong generalization capability, highlighting the potential of an effective RAG paradigm for real-world documents.