The present study was aimed at establishing the differences in the neurodevelopmental profile between two F2 lines derived from two F1 hybrid mouse strains (129 x C57BL/6 and C57BL/6 x SJL). The choice of the given strains was based on the frequent use of these mice in transgenic research. For the neurodevelopment phenotyping, we employed a test battery consisting of 23 somatometric, sensorial and motor tests. Significant variations between the strains were established in different functional domains. Some specific delays in the appearance of developmental landmarks were observed in F2 mice derived from crosses of F1 C57BL/6 x 129, whereas they acquired early developmental functions, such as the righting reflex, sooner than C57BL/6 x SJL-derived mice. C57BL/6 x 129 F2 offspring were spontaneously hypoactive, and their poorer motor performance was confirmed by low performance in the negative geotaxis test. However, there were no differences in the general psychomotor development as shown by the good performance in the homing test in both F2 lines. Both strains were susceptible to the handling procedures used, presenting a similar alteration in the response observed in the homing test as compared to nonhandled control mice. In conclusion, our work highlights the importance of the genetic background for transgenesis experiments and also the need for well-established testing protocols to obtain sufficient information at the first stage of behavioral screening of genetically modified mice.