Intra-lot and inter-lot variability in the spectra of levothyroxine was detected in the Drug Quality Study (DQS) using Fourier transform near-infrared spectrometry (FTNIR). Two vials of 12 vials sampled from Athenex lot AFN102 appeared 10.1 and 9.1 SDs from the center of the rest of the vials on the DQS FTNIR screening assay. Spectra of 108 vials from six lots in the library clustered in two groups (p=0.02), suggesting they represent different material.