The functional components of the lizard skull are divided into the chondrocranial braincase, protective dermatocranium, lower jaw, and hyobranchial apparatus. These regions are interconnected and become operational through the quadrate, a bone critical for cranial biomechanics and support of the peripheral auditory system. The quadrate is a complex and variable structure in squamates; however, neither the intraspecific nor interspecific variation of this element has been studied in detail. We investigated the intraspecific variation of quadrate morphology within Hemidactylus turcicus with the use of cleared and double-stained specimens and high-resolution x-ray microcomputed tomography. Our objectives were to quantify quadrate shape and the degree of intraspecific variation within this element with the use of 2-D and 3-D geometric morphometric analyses and investigate if this variation is driven by ontogeny and/or sexual dimorphism. Our results demonstrate that ontogeny, but not sexual shape dimorphism, drives the intraspecific variation of quadrate bone morphology in H. turcicus. We also illustrate the benefit of using 3-D morphometric analyses on complicated morphological structures. This is the first study to quantify the intraspecific variation of a single cranial element within geckos, and it highlights the importance of using increased sample sizes to further characterize the natural variation of skeletal morphology.