Background: Studies have shown that some children do not participate in sport or exercise because they did not establish early coordination and basic motor skills while at school. Basic motor skills form significant parts of the goals for students to achieve in the Swedish school subject Physical Education and Health (PEH). Aims: The aim was to study effects of an extension of physical activity and motor training, during a period of nine years, on motor skills and marks in the school subject PEH. Furthermore, a motor training program called "Motor Development as Ground for Learning" [Motorisk Utveckling som Grund for Inlarning] (MUGI) was tested and evaluated. Method: The study is longitudinal and two groups of students were followed during nine school years. At the start of the project the students were seven years old, and 15 years old at the follow-up. An intervention group (n = 161) had one scheduled lesson of physical activity and motor training every school day. A control group (n = 102) had the school's usual two PEH lessons per week. Motor skills observations were carried out in the school years 1, 2, 3, and 9 according to the MUGI checklists. Extra motor skill training, according to the MUGI model, was given to students in the intervention group who had motor skills deficits. The method was hypothetic-deductive and two hypotheses were tested: (1) Students' motor skills will improve with extended PEH and extra motor training according to the MUGI model, and (2) boys' and girls' marks in PEH will improve with extended PEH and extra motor training in school. Findings: The results confirmed the hypothesis that students' motor skills improve with extended physical activity and motor training. After only one year the students in the intervention group had significantly better motor skills (balance and coordination) than students in the control group. These differences remained and were also found at follow-up school years 3 and 9. Differences in motor skills between boys and girls decreased with extended physical activity and extra motor training in school. Significant correlations were found between motor skills school year 2, 3, and 9 and marks in PEH school year 9. The second hypothesis was confirmed by significantly higher marks in the school subject PEH school year 9 in the intervention than in the control group. Although there were no significant differences in motor skills between boys and girls in school year 9, girls had significantly lower marks in PEH than boys. Conclusions: The school has good potential for stimulating students' development of motor skills, but two lessons of PEH per week are not enough. Differences in motor skills between boys and girls may decrease with extended physical activity and extra motor training in school. The MUGI program can be useful as a pedagogic model for observing and improving motor skills in school. (Contains 3 tables and 3 figures.)