The Brazilian Sucro-energy Sector produces both energy, in the form of ethanol fuel, industrial steam and electricity, and sugar. Centro de Tecnologia Canavieira (CTC), the leading Brazilian sugarcane breeding company, has developed a pipeline of insect-protected sugarcane varieties to control sugarcane borer damage. The goal of this manuscript is to present the results of studies with three genetically modified (GM) sugarcane varieties and to evaluate the published literature regarding the possible presence of GM sugarcane DNA or protein in raw or refined sugar. Specifically, two varieties of approved GM sugarcane, CTC91087-6 and CTC175-A, and an experimental CTC variety, were grown in four individual plots to produce four batches each of processed raw sugar using standard smaller-scale laboratory processing methods resulting in a total of 12 independent batches of raw sugar. Herein, we report the development of event-specific probes and DNA detection methods, designed to detect the junction of sugarcane genomic DNA and the inserted DNA of the two approved GM varieties. An identical approach was used for the testing of sugar made from the experimental CTC variety. The methodology used TaqMan® real-time PCR and ELISA assays validated for the four GM proteins expressed by these three events (Cry1Ab, Cry1Ac, NPTII, and PAT (bar)). The developed assays had very low limits of detection (LODs) for the various event-specific DNA probes (7.2–25 ng/g sugar) and insecticidal and selectable marker proteins (2.9–10.9 ng/g sugar). No event-specific DNA and no GM proteins were detectable in the 12 independent batches of raw sugar produced from these three GM sugarcane events. The results of this study, using very sensitive methods and testing several sugar batches, extend the conclusions of previous studies, reviewed herein, that showed the extensive degradation and removal of DNA and protein during sugarcane processing. Overall, these results indicate that there are no distinguishable differences between the highly purified, chemically defined sugar produced from conventional or GM varieties.