Following the successful event represented by the 2nt International Workshop on Privacy and Security of Big Data (PSBD 2015), held in conjunction with the 2015 IEEE International Conference on Big Data (BigData 2015), in Santa Clara, CA, USA, during October 29, 2015, and the 1st International Workshop on Privacy and Security of Big Data (PSBD 2014), held in conjunction with The 23rd ACM International Conference on Information and Knowledge Management (CIKM 2014), in Shanghai, China, during November 7, 2014, the 3rd International Workshop on Privacy and Security of Big Data (PSBD 2016) focuses the attention on privacy and security research issues in the context of Big Data, a vibrant and challenging research context which is playing a leading role in the Database research community. Indeed, while Big Data is gaining the attention from the research community, also driven by some relevant technological innovations (like Clouds) as well as novel paradigms (like social networks), the issues of privacy and security of Big Data represent a fundamental problem in this research context, due to the fact Big Data are typically published online for supporting knowledge management and fruition processes and, in addition to this, such data are usually handled by multiple owners, with possible secure multi-part computation issues. Some of the hot topics in the context privacy and security of Big Data include: (i) privacy and security of Big Data integration and exchange; (ii) privacy and security of Big Data in data-intensive Cloud computing; (iii) system architectures in support of privacy and security of Big Data, e.g., GPUs: (iv) privacy and security issues of Big Data querying and analysis.