It is aimed in this study to analyze the effects of the Montessori education method on children with Down syndrome and autism having special training who have received and not received Montessori education through the Eurofit test batteries selected for motor skills and physical fitness. A total of 20 male children with Down syndrome and autism in the age range of 12 to 16 and receiving and not receiving Montessori education at two different special education and rehabilitation centers in Kayseri were included in the study. The treatment group included a total of 10 children, 5 with Down syndrome and 5 with autism, and the control group of 10 children, 5 with Down syndrome and 5 with autism. While the volunteers included in the treatment group received Montessori education, those included in the control group received a traditional education. In the study, the volunteers performed the selected Eurofit tests including flamingo balance, plate tapping, sit and reach, handgrip and standing long jump tests. When the results of the Eurofit test batteries of the treatment and control groups were examined, plate tapping and standing long jump test results were found significant in the comparison of the pretest and posttest of the treatment group (p < 0.05). In the pretest and posttest comparison of the control group students, a significant difference was determined in the sit and reach test (p < 0.05). In the posttest comparison of the control and treatment groups, a statistically significant difference was determined between the pretest and posttest measurements of the plate tapping and between the pretest and posttest measurements of the standing long jump (p<0.05). In the pretest comparison of the control and treatment groups, no statistically significant difference was found between the pretest and posttest of flamingo balance, pretest and posttest of plate tapping, pretest and posttest of sit and reach, pretest and posttest of standing long jump and pretest and posttest of handgrip measurements of the control and treatment groups (p>0.05). Consequently, the use of Montessori education materials supports the big and small muscle groups of children with disabilities since most of them learn about an object through touch. In our study, when some activity and motor skills of the children with down syndrome and autism in the special rehabilitation school that uses the Montessori education method were analyzed, it was observed that there was an improvement in their physical activities and some motor skills according to the results of plate tapping, standing long jump and sit and reach tests. It is recommended that education programs can be prepared by using Montessori Approach as part of the education programs applied in preschool education institutions and that they can be used more widely together with traditional education programs.