Isogenic, or inbred, mouse strains are currently the experimental subjects of choice in laboratory studies focused on genetics, pharmacology, and psychological issues. Understanding phenotypic differences in isogenic strains is important in order to interpret experimental results obtained from inbred mouse strains. Four commonly used inbred strains, C57BL/6NHsd (C57), DBA/2NHsd (DBA), 129S2/SvHsd (129), and Balb/cAnHsd (Balb/c), are investigated in this study using four different behavioral tasks that measure locomotor activity and cognitive behavior (Morris Water Maze (MWM), T-maze, and operant autoshaping procedures). In the locomotor activity task 129 mice showed significantly less horizontal ambulation than any other strain, while differences in rearing was seen between all strains, with C57 mice producing the most, and 129 showing the least rearing. Thigmotaxia was seen the most in the 129 strain, less so with the Balb/c and DBA strains, and the least in the C57 mice. In the MWM learning across strains was noted but there was no difference between the strains. In the T-maze the Balb/c strain showed the shortest latency to enter an arm, while the 129 strain showed the longest. As expected they also showed the lowest accuracy and the highest percent time-outs compared to all the other strains. In the autoshaping procedure little difference between the strains was observed. Balb/c mice trended graphically towards higher rates however there was no difference with regard to number of contingent responses or number per strain to reach a criterion of 10 or more contingent reinforcers. Finally, locomotor activity was measured again at the end of the study. The activity results were still similar, although the C57 strain showed a decrease in horizontal ambulation as compared to DBA and Balb/c strains; however, the 129 strain still showed the least activity. These results indicate that there are significant differences in locomotor behavior and cognitive processes in these strains that should be considered when interpreting results from studies using these inbred mouse strains.