Researchers who study the selection and breeding program criteria for military working dogs aim to help maximize the years of active duty service. Computed tomographic (CT) quantitative phenotyping has been previously described as a method for supporting these research studies. Funnel-shaped lumbar vertebral foramen malformations have been previously described in Labrador retriever military working dogs and proposed to be risk factors for impaired arterial perfusion of nerve tissues during exercise. Articular process dysplasia malformations have been previously described in varying dog breeds and proposed to be risk factors for articular process degenerative joint disease and vertebral foramen stenosis. Aims of this retrospective, cross-sectional study were to describe quantitative CT phenotyping methods for characterizing funnel-shaped lumbar vertebral foramina and articular process dysplasia malformations and to apply these methods in a comparison between groups of German shepherd and Belgian Malinois military working dogs. A military working dog hospital's database was searched for German shepherd and Belgian Malinois dogs aged <6 years that had CT scans of the lumbosacral region during the period of 2008–2016. Observers unaware of CT findings recorded available clinical data for each of the dogs. An observer unaware of clinical data recorded CT measures of funnel-shaped lumbar vertebral foramina and articular process dysplasia malformations for each of dogs and each of the lumbar vertebrae that were available in the scans. A total of 59 dogs were sampled: 41 German shepherd and 18 Belgian Malinois. Articular process dysplasia and funnel-shaped vertebral foramen phenotypic traits were present in both breeds in this sample, with the frequency and quantitative measure of these traits being greater in German shepherd dogs and heavier dogs. Lower weight dogs had a lesser degree of a funnel-shaped foramen at all sampled vertebral locations. A consistent relationship between articular process dysplasia measures ...