This whitepaper presents the T-REX protocol, which is designed for the compliant issuance and management of permissioned tokens, specifically focusing on tokenized securities. The document outlines the need for such a protocol in the context of evolving financial markets that seek efficiency, accessibility, and liquidity similar to that of cryptocurrencies. It emphasizes that unlike utility tokens, security tokens must adhere to regulatory compliance, including Know Your Customer (KYC) and Anti-Money Laundering (AML) requirements. The ERC3643 token standard and its T-REX implementation are introduced as solutions to these challenges. The paper details a 'Compliance by Design' approach, ensuring that investors cannot hold digital securities without meeting compliance requirements. It further explains the role of ONCHAINID, a blockchain-based identity management system, and the Eligibility Verification System (EVS) in managing compliant transactions. The document concludes by highlighting the innovative mechanisms embedded within the T-REX protocol that facilitate secure and transparent management of security tokens.