The aim of the conducted research was to determine differences between eleven year old female and male pupils of the same age in motor skills tests, constructed based on representative teaching topics defined by the official Physical Education syllabus for the fifth grade, and to determine if the morphological characteristics and motor abilities have any effect on the mentioned gender differences. The sample of subjects included 146 fifth-grade female pupils and 149 fifth-grade male pupils from a primary school in Split, aged 11 (± 6 months). Data collection was implemented by the application of 16 morphological measurements, 21 motor abilities test and 7 motor skills test. The applied variables had satisfactory metric characteristics and enabled data collection of scientifically valid data. The analysis of univariate differences of motor skills showed that on average the female pupils got statistically better grades than the male pupils for handstand near the vertical surface, while the male pupils achieved better results for overshoulder forward fall on the dominant side, basic floor shot (handball) and standing one hand shot (basketball). Discriminant analysis of significant differences between female and male pupils without and with the removed impact (variance decomposition) of morphological characteristics and motor abilities for each motor skill variable indicates that all the gender differences regarding motor skills are statistically significant, and they are decreased only when exclusion of morphology and motor activities occur. Parallel exclusion of impact of both morphology and motor activities of gender differences on motor skills additionally and significantly decreases up to a limit value of statistical significance. The greatest contribution to the overall multivariate differences can be seen in basic floor shot (handball) and standing one hand shot (basketball). When eliminated the impact only of morphology the structure of discriminant function, and therefore the structure of differences between the genders, did not essentially change in regards to the structure of differences obtained when eliminated only motor activities, but only when additionally eliminated morphology and motor activities as well. Elimination of impact of motor activities on gender differences changed contributions, and mostly in favour of high jump (scissors technique) and handstand near the vertical surface.The analysis of covariance was used to test a univariate size of contribution for each morphological and motor factor on differences between female and male pupils in performing motor skills. With this purpose factorisation of morphological and motor variables was performed and it resulted in four morphological and six motor factors. As far as morphological factors are concerned the middle size of impact on gender differences for the monitored motor skills has a voluminosity while the remaining three morphological factors are small in size as far as their activity is concerned. The voluminosity factor also acts statistically significant on gender differences for all motor skills, while the transverse dimension of the skeleton acts on the majority of motor skills and fat tissue on a few motor skills, the transverse dimension of the skeleton does not show differences for any motor skill. As far as the motor factors are concerned the middle size of impact on gender differences for all the observed motor skills was found in explosiveness, while the other motor factors had a small size of impact. Explosiveness acts statistically significant on gender differences for all the observed motor skills, while strength and frequency of movement acts on the majority of motors skills, and the other factors of differences on a smaller number of the variables. For testing the structure of impact of morphological characteristics and motor abilities on differences between female and male students in performing the motor skills, a two-way 3x2 variance analysis was used and for this purpose groups were formed based on low, middle and high results of morphological and motor factors. This provided an additional insight of the highest or lower impact of morphological and motor factors on differences of female and male pupils for each motor skill. In conclusion, the results of this study show that morphology and motor activities equally impact gender differences in both female and male pupils when performing motor skills and individual or group elimination of morphology or motor activities brings to a similar structure found in the other multivariate differences.