Large language models (LLMs) have achieved significant performance progress in various natural language processing applications. However, LLMs still struggle to meet the strict requirements for accuracy and reliability in the medical field and face many challenges in clinical applications. Existing clinical diagnostic evaluation benchmarks for evaluating medical agents powered by LLMs have severe limitations. To address these limitations, we introduce ClinicalLab, a comprehensive clinical diagnosis agent alignment suite. ClinicalLab includes ClinicalBench, an end-to-end multi-departmental clinical diagnostic evaluation benchmark for evaluating medical agents and LLMs. ClinicalBench is based on real cases that cover 24 departments and 150 diseases. We ensure that ClinicalBench does not have data leakage. ClinicalLab also includes four novel metrics (ClinicalMetrics) for evaluating the effectiveness of LLMs in clinical diagnostic tasks. We evaluate 17 general and medical-domain LLMs and find that their performance varies significantly across different departments. Based on these findings, in ClinicalLab, we propose ClinicalAgent, an end-to-end clinical agent that aligns with real-world clinical diagnostic practices. We systematically investigate the performance and applicable scenarios of variants of ClinicalAgent on ClinicalBench. Our findings demonstrate the importance of aligning with modern medical practices in designing medical agents.