Noise reactivity is a common problem for dogs, and may progress to true phobia. Survey studies report that some type of noise reaction occurs in up to half of all pet dogs throughout their lifetimes, indicating that noise reactivity/phobia is a welfare issue. Familial aggregations of affected dogs have been reported and increased prevalence in certain breeds has been suggested. Reactivity to noise can severely compromise function in both pet and working dogs. Noise reactivity may be co-morbid with many anxiety disorders for both canines and humans and is postulated to effect information processing in associated human, rodent and dog conditions. Any putative effect of noise on information processing becomes a concern for problem solving and other aspects of cognition that are important to working dogs. Accordingly, we sought to phenotype 3 breeds of herding dogs commonly used for work as detection dogs, police/patrol dogs, search and rescue dogs, and/or service dogs: Australian shepherds (AUS), Border collies (BOC) and German shepherds (GSD). We analyzed demographic information and behavioral responses to noises (guns, storms, fireworks) known to provoke fearful or phobic responses for 59 AUS, 81 BOC, and 58 GSD, who were also included in a genetic analysis. Behaviors were compared using a metric constructed from information on type, frequency and intensity of response, the Anxiety Intensity Rank (AIR score). Reactivity to noise was found to segregate in some family lines for the dogs in this study, although individuals expressed considerable variation in noise response. Such variation may be time and exposure dependent and presents a phenotyping challenge. In this study, the presence and intensity of reactivity as represented by AIR scores varied by breed, but only slightly with age. The BOC studied were older, and BOC and AUS were more severely affected (higher AIR scores) than were GSD. Source/purpose of dog may also affect severity of affliction. Determination of crisp, accurate phenotypes is essential for understanding underlying genetic contributions. For noise reactivity/phobia accurate phenotypes include age of onset and specific behavioral characterization. Standardized, objective assessments are essential for assessment of progression and co-morbidity. Our data imply that accurate phenotypic assessment is possible at a relatively early age, providing for both humane treatment and accurate phenotyping that facilitates good genotyping.