Lithuania combines strong human-capital and selected innovation indicators with comparatively weak patent performance. According to the European Innovation Scoreboard 2026, Lithuania reaches 86.6% of the EU average in overall innovation performance, while PCT patent applications amount to only 40.4%. This article examines the factors associated with this apparent patent paradox, using Estonia, Latvia and Poland as comparative cases. Drawing on European Innovation Scoreboard data, supplemented by European Commission, EPO, WIPO and Eurostat evidence and recent scholarly literature, the study applies a research-to-patent conversion framework linking innovation inputs, business R&D, science-business interaction, and intellectual-property outputs. The findings indicate that Lithuania’s patent gap is associated with low business R&D intensity, relatively weak science-business linkages, fragmentation of the public research base, technology-transfer capacity, sectoral structure and commercialisation constraints. Comparative evidence suggests that stronger R&D inputs alone are insufficient without effective knowledge-transfer mechanisms.