GWAS using the two-step imputation confirmed known associations on thyroid traits and revealed novel loci for thyroid volume (<i>TG, PAX8, IGFBP5, NRG1</i>), and goiter (<i>XKR6</i>), the latter not significant in the conventional imputation.<h4>Availability and implementation</h4>The study provides a workflow for high-quality imputation results without batch effects, fostering genetic analysis involving multiple genotyping arrays. Here, PAX8 is linked to goiter.