Irf6 (interferon regulatory factor 6) is expressed in tooth buds and palatine rugae during development in the mouse. Here we report the first study to investigate whether IRF6 variation is associated with palatine rugae patterns in a population with sporadic tooth agenesis. Fifty-two individuals with sporadic tooth agenesis and their parents were studied. Palatine rugae were scored from casts available for a subset of 38 families. DNA samples were obtained from whole blood or saliva samples. Genotyping was performed using TaqMan assays. Linkage disequilibrium and transmission distortion analyses of the marker alleles were performed. Borderline results were obtained for IRF6 genetic variation and having primary rugae larger on the right side than on the left (rs20131633, P = 0.07; rs642961, P = 0.06) and having fewer than eight primary palatine rugae (rs20131623, P = 0.07). However, no specific pattern of tooth agenesis was associated with the palatine rugae patterns studied. Our data suggest that IRF6 may contribute to specific palatine rugae patterns in humans.