Background: The Chihuahua dog breed is known for frequent occurrence of a bregmatic fontanelle on the dorsal skull. A common conception is that this skull defect is clinically irrelevant in Chihuahuas. No studies, however, describe the prevalence of this malformation, whether it is accompanied by fontanelles at other locations on the skull or how to assess the severity of these lesions. Our primary aim was, by using computed tomography imaging, to describe the presence, number, and location of persistent fontanelles (PF) at cranial sutures on dorsal, lateral and caudal cranial surfaces in Chihuahuas. The secondary aim was to develop a method to measure the fontanelle area in computed tomography images by using the closed polygon tool of Osirix Medical Imaging Software. Results: Of the 50 dogs evaluated, 46 (92%) had either one or several PFs. The mean ± SD number of affected cranial sutures per dog was 2.4 ± 2.3 (range 0-10), and mean ± SD number of PFs was 2.8 ± 3.0 (range 0-13). Of the 46 dogs with affected sutures, 7 (15%) had no PF at a location typical for a bregmatic fontanelle. The inter-rater reliability of the fontanelle area measurement was almost “perfect”, and intra-rater reliability reached “excellent” agreement. Conclusions: PFs are almost ubiquitous in the examined group of Chihuahuas. They are located at dorsal, lateral, and caudal surfaces of the cranium, and hence are not all recognized reliably by palpation in adult dogs. Though the pathogenesis of the PFs described here is unknown, bone-deficient lesions may occur due to congenital defects in cranial bone ossification, delayed closure of cranial sutures, or bone resorption, as is observable in children with craniosynostosis (premature cranial suture closure). Because the imaging findings described in the Chihuahuas of this study are similar to findings among children with craniosynostosis/premature cranial base synchondrosis closure, this growth disorder may be a predisposing factor for the PFs described here. Further studies are necessary to evaluate the pathogenesis and clinical relevance of these lesions. Due to high inter- and intra-rater reliability of the method of fontanelle area measurement it may be useful in future studies.