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This study aimed to compare the color changes in two different orthodontic clear aligner systems after submersion in various beverages for 14 days. The tested aligner systems were Taglus Premium made of polyethylene terephthalate glycol (the TAG group) and CA ® Prodin+ made of a transparent copolyester and a thermoplastic elastomer (the PRO group). A total of 56 samples were firstly divided into two groups according to the tested system-TAG and PRO. Each group was subsequently divided in four subgroups according to immersion solution: A-artificial saliva, B-cola, C-coffee, D-red wine. Color measurements were performed on Days 1, 7 and 14 using a portable colorimeter and the CIE L*a*b* system. The obtained results showed significant color changes in both materials when exposed to coffee and red wine ( p > 0.05). Samples in the PRO group showed a greater susceptibility to discoloration (higher ΔE values) when compared to the TAG group after submersion in cola ( p = 0.025), coffee ( p = 0.005) and red wine ( p = 0.041) solutions. Statistical analysis revealed that all of the color parameters ΔL*, Δa*, Δb* and ΔE of both tested materials were affected by submersion in coffee solution for 14 days. In conclusion, the CA ® Pro+ aligner system is more prone to staining compared to the Taglus material after submersion for 14 days in cola, coffee and red wine solutions. Submersion for 14 days in coffee solution alters all of the color parameters (ΔL, Δa, Δb and ΔE) of both tested aligner materials.