The homeodomain transcription factor Nkx6-1 is essential for proper motor neuron development and development of insulin-producing pancreatic beta-cells. Nkx6-1 is closely related to Nkx6-2 and Nkx6-3, and all three are expressed in the developing central nervous system and in the developing foregut. Immunohistochemical detection of protein expression is an important tool for description of the temporal differences in expression patterns. When several gene family members like the Nkx6 factors have overlapping or juxtaposed expression domains, there is an elevated risk of unrecognized cross-reactivity, and it is therefore crucial to determine the specificities of antibodies against such targets. In this study we have determined the epitope consensus sequences of four monoclonal antibodies against Nkx6-1 using SPOT membranes, and we refined the results by combined peptide recognition and blocking assays. We show that two of the monoclonal anti-Nkx6-1 antibodies specifically recognize Nkx6-1 and do not cross-react to Nkx6-2 and Nkx6-3. The other two monoclonal anti-Nkx6-1 antibodies are specific to Nkx6-1 in mice but do not recognize Nkx6-1 in chicken and human.