Ciguatoxins (CTXs) are naturally occurring neurotoxins that can accumulate in fish and cause Ciguatera Poisoning (CP) in seafood consumers. Ciguatoxic fish have been detected in tropical and subtropical regions of the world including the Pacific and Indian Oceans, the Caribbean Sea, and more recently in the northeast Atlantic Ocean. The biogeographic distribution of ciguatoxic fish appears to be expanding; however, the paucity of CTX standards and reference materials limits the ability of public health authorities to monitor for these toxins in seafood supply chains. Recent reports establish that Caribbean Ciguatoxin-1 (C-CTX1) is the principal toxin responsible for CP cases and outbreaks in the northeast Atlantic Ocean and that C-CTX congener profiles in contaminated fish samples match those from the Caribbean Sea. Therefore, in this work, C-CTX reference materials were prepared from fish obtained from the northeast Atlantic Ocean. The collection of fish specimens (e.g., amberjack, grouper, or snapper) was screened for CTX-like toxicity using the in vitro sodium channel mouse neuroblastoma cytotoxicity assay (N2a cell assay). Muscle and liver tissues from toxic specimens were pooled for extraction and purified products were ultimately profiled and quantified by comparison with authentic C-CTX1 using LC-MS/MS. This work presents a detailed protocol for the preparation of purified C-CTX reference materials to enable continued research and monitoring of the ciguatera public health hazard. To carry out this work, C-CTX1 was isolated and purified from fish muscle and liver tissues obtained from the Canary Islands (Spain) and Madeira archipelago (Portugal).