Pax8 is a transcription factor that plays an important role in the regulation of genes that are exclusively expressed in differentiated thyroid cells. In the thyroid cell environment, evidence exists that Pax8 is part of a multiprotein complex in which its transcriptional activity may be modulated by specific co-factors. In an attempt to identify proteins that interact with Pax8, we performed pull-down experiments challenging the GST–Pax8 fusion protein with protein extracts prepared from the thyroid differentiated cell line PC Cl3. By this approach, we isolated a 113-kDa protein that is able to associate with Pax8, which was further identified by mass fingerprint experiments as poly(ADP-ribose) polymerase 1 (PARP1). To further confirm this interaction, we also showed that PARP1 can be co-immunoprecipitated with Pax8 in vivo from a thyroid cell extract. Gel shifts experiments demonstrated that PARP1 binding to Pax8 significantly inhibits Pax8 binding to DNA. Accordingly, we provide evidence that the functional outcome of such an interaction is a significant downregulation of Pax8 transcriptional activity. In the context of thyroid-specific gene transcription, our results suggest that PARP1 behaves as an important negative co-factor involved in the regulation of Pax8-dependent gene expression.