Evidence suggests that paw preferences are related to emotional functioning in the domestic dog. Whether motor bias in this species is related to the display of behaviour problems, which often have their basis in emotional reactivity, is still unknown. This study therefore explored the relationship between lateralised motor behaviour in the form of paw preferences and the occurrence of canine behaviour problems. Fifty-two dogs presenting with one or more behaviour problems, and 61 control animals, had their paw preferences assessed using the commonly employed KongTM ball test. The dogs’ behavioural profile was determined using the C-BARQ, a psychometric tool designed to provide standardized evaluations of canine behaviour. Analysis revealed a roughly equal split in the proportion of dogs classified as ambilateral and lateralised, although dogs were more like to be ambilateral than left- or right-pawed. Dogs differed significantly in their behavioural profile, with animals in the behaviour problem group displaying more severe patterns of stranger- and dog-directed aggression and fear, non-social fear and touch sensitivity than those in the control group. There was no significant difference in the distribution, direction or strength of the dogs’ paw use between the two groups of animals. The dogs’ paw preference classification was significantly associated with one of the C-BARQ subscale scores, namely stranger-directed aggression, with left-pawed dogs having lower scores on this subscale than right-pawed or ambilateral animals. The direction of the dogs’ paw use in the behaviour problem group was significantly correlated with C-BARQ scores for the subscales of stranger-directed aggression, stranger-directed fear and attention-seeking behaviour, with higher subscale scores associated with increasing right-pawedness. There was no significant correlation between the direction of the dogs’ paw use and any of the other C-BARQ subscale scores. The strength of the dogs’ paw preferences was not significantly correlated with any of the C-BARQ subscale scores for either the control or behaviour problem group of animals. Canine sex was not significantly related to either the dogs’ paw preferences or the presentation of behaviour problems. Overall, this study provides little evidence in support of a relationship between paw preference and the occurrence of behaviour problems in the domestic dog. Further, longitudinal, work is recommended in an effort to unravel the ontogeny of lateralisation and its association with emotional reactivity in this species.