While our results suggest LADA is genetically closer to T1D than to T2D, we observed an association at one T2D locus, HNF1A, known to be associated with T2D and ‘maturity-onset diabetes of the young’; strikingly, the HNF1A signal remained significantly associated with LADA even in the cohort enriched for both T1D autoantibodies. Here, HNF1A is linked to type 2 diabetes mellitus.