With the rapid growth of machine learning and artificial intelligence in medical cloud systems, cloud-aided medical computing has materialized a concrete platform for rapid realization of the service-oriented computing paradigm. However, using machine learning approaches in medical clouds might cause serious privacy leakage risk, for example, it needs to take the patients’ sensitive data as the inputs of the machine learning algorithm. In this article, we propose an efficient and privacy-preserving clinical diagnosis scheme that was performed by an (untrusted and malicious) outsourced cloud platform, which can provide the diagnosis assistance for doctors without leaking any sensitive information of patients and service providers. Concretely, we give the security model of privacy-preserving multiclass support vector machine (SVM) in outsourced medical clouds and design a secure clinical diagnosis scheme with privacy-preserving multiclass predecision and diagnosis. We propose a novel encoding approach to implement the encryption of negative number, and design several security building blocks, such as privacy-preserving decision function computing, privacy-preserving classification, and search of max decision function on encrypted fields, to provide the construction of the secure clinical diagnosis with privacy-preserving multiclass SVM. We give the concrete scheme and provide the experiment on Dermatology datasheet. Security analysis and experimental results indicate that the proposed scheme is efficient and practical in privacy-preserving clinical diagnosis systems.